Hepatocyte Nuclear Factor 4‐Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver
Open accessAbstract
Cell‐fate determination is influenced by interactions between master transcription factors (TFs) and cis‐regulatory elements. Hepatocyte nuclear factor 4 alpha (HNF4A), a liver‐enriched TF, acts as a master controller in specification of hepatic progenitor cells by regulating a network of TFs to control onset of hepatocyte cell fate. Using analysis of genome‐wide histone modifications, DNA methylation, and hydroxymethylation in mouse hepatocytes, we show that HNF4A occupies active enhancers in hepatocytes and is essential for active histone and DNA signatures, especially acetylation of lysine 27 of histone 3 (H3K27ac) and 5‐hydroxymethylcytosine (5hmC). In mice lacking HNF4A protein in hepatocytes, we observed a decrease in both H3K27ac and hydroxymethylation at regions bound by HNF4A. Mechanistically, HNF4A‐associated hydroxymethylation (5hmC) requires its interaction with ten‐eleven translocation methylcytosine dioxygenase 3 (TET3), a protein responsible for oxidation from 5mC to 5hmC. Furthermore, HNF4A regulates TET3 expression in liver by directly binding to an enhancer region. Conclusion : In conclusion, we identified that HNF4A is required for the active epigenetic state at enhancers that amplifies transcription of genes in hepatocytes.
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Written from the paper’s full text.
TL;DR
HNF4A occupies active enhancers in mouse hepatocytes and is required to maintain H3K27ac and 5hmC at those regions. It physically interacts with TET3 and directly regulates Tet3 expression, linking a master liver transcription factor to an active enhancer epigenetic state.
Key findings
- HNF4A binding in hepatocytes was predominantly intronic (47.35%) and distal intergenic (33.33%), with only 9.81% at promoters; bound regions were enriched for H3K4me1, H3K27ac, DNase I hypersensitivity, and 5hmC but depleted of 5mC.
- In hepatocyte-specific HNF4A conditional knockout livers, H3K27ac decreased at all examined HNF4A-bound sites, and 5hmC fell by almost twofold at both HNF4A-only and shared HNF4A/FOXA2 regions; 5mC increased at most loci, especially HNF4A-only sites.
- During hepatoblast-to-hepatocyte differentiation, 2,765 hepatocyte-specific HNF4A-bound regions gained H3K27ac and 5hmC and lost 5mC, and associated genes were more highly expressed in hepatocytes.
- HNF4A co-immunoprecipitated with TET3 in HepG2 cells, HEK293T cells, and mouse hepatocyte/hepatoblast nuclear lysates; proximity ligation assays confirmed nuclear association in vivo. HNF4A bound an intronic Tet3 enhancer, and HNF4A knockdown reduced Tet3 mRNA and protein, while reporter assays showed HNF4A-dependent enhancer activity.
Methods
- Genome-wide profiling used ChIP-seq for HNF4A, H3K4me1, H3K4me3, and H3K27ac, plus MeDIP-seq and hMeDIP-seq for 5mC and 5hmC, in mouse hepatocytes and E14.5 hepatoblasts; selected loci were validated by qPCR.
- Loss-of-function experiments used tamoxifen-inducible hepatocyte-specific Hnf4a conditional knockout mice (6–8 weeks old) and siRNA-mediated HNF4A knockdown in HepG2 cells.
- Protein interaction and regulatory assays included co-immunoprecipitation, proximity ligation assay, and luciferase reporter assays with mouse and human TET3 enhancer regions; qPCR data were analyzed by Student’s t-test with p<0.05 considered significant, using at least three independent experiments.
Limitations
- The paper states that it focused on TET3 even though TET2 is also expressed in liver, and that other oxidized DNA derivatives such as 5-formylcytosine and 5-carboxylcytosine were not examined; future work on the full 5mC oxidation pathway is needed.
- The paper notes that whether HNF4A-dependent H3K27ac and 5hmC changes occur together or independently remains unresolved.
- The paper reports only a small 5mC increase in HNF4A knockout livers, suggesting that 5mC recovery may be slower than 5hmC loss or may not occur; it also notes that 5hmC is much less abundant than 5mC, which may make whole-liver 5mC changes hard to detect. Evident from the text, most mechanistic work relies on mouse hepatocytes and HepG2/HEK293T cells rather than human liver tissue.
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Claims the paper makes
34 of 45 cited sources checked · 21 supported · 2 flagged · accuracy not yet measured
- Premisecitation
In adult mice, loss of HNF4A affects lipid homeostasis leading to liver steatosis.
“HNF4A deficiency in mouse embryonic liver causes failure in hepatocyte differentiation (2), while in adult mice loss of HNF4A affects lipid homeostasis leading to liver steatosis (5).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [5] Hayhurst GP, Lee YH, Lambert G, Ward JM, Gonzalez FJ. Hepatocyte nuclear factor 4alpha (nuclear receptor 2A1) is essential for maintenance of hepatic gene expression and lipid homeostasis. Mol. Cell. Biol. 2001; 21: 1393– 403. 11158324 PMC99591 source
- Premisecitation
There is a significant overlap between HNF4A and FOXA2 bound regions in hepatocytes.
“We previously reported a significant overlap between HNF4A and FOXA2 bound regions (FBRs) in hepatocytes (11).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [11] Alder O, Cullum R, Lee S, Kan AC, Wei W, Yi Y, Hippo signaling influences HNF4A and FOXA2 enhancer switching during hepatocyte differentiation. Cell Rep. 2014; 9: 261– 271. 25263553 PMC4612615 source
- Findingown data
Genes associated with active clusters showed higher expression than Cl5.
“We looked at expression of genes with transcriptional start sites (TSSs) within 20kb of a bound region using RNA-seq data from hepatocytes (11) and not surprisingly found that genes associated with these active clusters showed higher expression than Cl5, which lacks evidence of active, open chromatin (Fig. 2F).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [11] Alder O, Cullum R, Lee S, Kan AC, Wei W, Yi Y, Hippo signaling influences HNF4A and FOXA2 enhancer switching during hepatocyte differentiation. Cell Rep. 2014; 9: 261– 271. 25263553 PMC4612615 source
- Premisecitation
HNF4A is a key TF in liver as its loss is associated with transcriptional repression of genes.
“HNF4A is a key TF in liver as its loss is associated with transcriptional repression of genes (5, 10).”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [5] Hayhurst GP, Lee YH, Lambert G, Ward JM, Gonzalez FJ. Hepatocyte nuclear factor 4alpha (nuclear receptor 2A1) is essential for maintenance of hepatic gene expression and lipid homeostasis. Mol. Cell. Biol. 2001; 21: 1393– 403. 11158324 PMC99591 source
- cites [10] Watt A, Garrison WD, Duncan SA. HNF4: A central regulator of hepatocyte differentiation and function. Hepatology. 2003; 37: 1249– 1253. 12774000 source
- Interpretationcitation
HNF4A plays a role in the establishment of active enhancers.
“This supports a role of HNF4A in the establishment of active enhancers(39).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [39] Rollini P, Fournier RE. The HNF-4/HNF-1alpha transactivation cascade regulates gene activity and chromatin structure of the human serine protease inhibitor gene cluster at 14q32.1. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 10308– 13. 10468604 PMC17884 source
The Results report that introducing HNF-4 induced expression-associated DNase I hypersensitive sites and established active-locus chromatin structure in the α1AT/ATR/CBG region (page unavailable). However, the Discussion says the functions of individual regulatory elements remain to be defined. The paper supports a role in chromatin remodeling, but does not establish that the induced sites are active enhancers. (LLM, conf=0.85)
Experimental — accuracy not yet measured
- Interpretationcitation
HNF4A may regulate chromatin indirectly by controlling the expression of chromatin remodelling genes, such as Smarcd3 and Cdt1.
“In addition, HNF4A may regulate chromatin indirectly by controlling the expression of chromatin remodelling genes, such as Smarcd3 and Cdt1, as their expression is altered in HNF4A KO livers (40).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [40] Holloway MG, Miles GD, Dombkowski AA, Waxman DJ. Liver-specific hepatocyte nuclear factor-4alpha deficiency: greater impact on gene expression in male than in female mouse liver. Mol. Endocrinol. 2008; 22: 1274– 86. 18276827 PMC2366185 source
- Findingown data
HBRs demonstrate high enrichment of H3K4me1 and H3K27ac flanking these regions, suggestive of active enhancers.
“Examination of HBRs demonstrated a high enrichment of H3K4me1 and H3K27ac flanking these regions (Fig. 1A), suggestive of active enhancers.”
Quote in the paperSubstantial claim - Findingown data
Clusters 1, 2, 3 and 4 displayed almost identical patterns of histone and DNA modifications indicating open and active chromatin states.
“Cluster 1, 2, 3 and 4 displayed almost identical patterns of histone and DNA modifications indicating open and active chromatin states.”
Quote in the paperSubstantial claim - Findingown data
In mice lacking HNF4A protein in hepatocytes, there is a decrease in both H3K27ac and hydroxymethylation at regions bound by HNF4A.
“In mice lacking HNF4A protein in hepatocytes, we observed a decrease in both H3K27ac and hydroxymethylation at regions bound by HNF4A.”
Quote in the paperSubstantial claim - Findingown data
HNF4A regulates TET3 expression in liver by directly binding to an enhancer region.
“Furthermore, HNF4A regulates TET3 expression in liver by directly binding to an enhancer region.”
Quote in the paperSubstantial claim - Findingown data
Cl1 is enriched for H3K4me1, H3K27ac and 5hmC but depleted for 5mC compared to Cl5.
“Further, these clusters revealed distinctive histone and DNA signature patterns with Cl1 being enriched for H3K4me1, H3K27ac and 5hmC but depleted for 5mC compared to Cl5 (Fig. 2A).”
Quote in the paperSubstantial claim - Findingown data
HNF4A preferentially binds to intronic (47.35%) and distal intergenic regions (33.33%) with a small proportion at gene promoters (9.81%).
“Analysis of HNF4A ChIP-seq data revealed its preferential binding to intronic (47.35%), and distal intergenic regions (33.33%) with a small proportion at gene promoters (9.81%) (Fig. S1A).”
Quote in the paperNot a substantial claim - Findingcitation
Mouse liver DNase-seq data shows very high signals, demonstrative of open chromatin at HBRs.
“The active status of these enhancers was further confirmed by examination of mouse liver DNase-seq data (ENCODE), which shows very high signals, demonstrative of open chromatin at HBRs (Fig. S1B).”
Quote in the paperNot a substantial claim - Findingown data
Cl5 regions show the least chromatin accessibility of all clusters based on DNaseI-seq data from mouse liver.
“Furthermore, Cl5 regions show the least chromatin accessibility of all clusters based on DNaseI-seq data from mouse liver (Fig. S2A).”
Quote in the paperNot a substantial claim - Findingown data
RXRA, ESRB and HINFP motifs were enriched in HNF4A bound regions which lack FOXA2.
“Moreover, we observed that RXRA, ESRB and HINFP motifs were enriched in HNF4A bound regions which lack FOXA2.”
Quote in the paperNot a substantial claim - Findingown data
The TET3-HNF4A interaction was observed in nuclear lysates isolated from mouse hepatocytes and hepatoblasts.
“Importantly, the TET3-HNF4A interaction was observed in nuclear lysates isolated from mouse hepatocytes (Fig. 5D) as well as hepatoblasts (Fig. 5E).”
Quote in the paperSubstantial claim - Findingown data
We did observe a clear gain in 5mC in HepG2 cells upon HNF4A knockdown.
“However, we did observe a clear gain in 5mC in HepG2 cells upon HNF4A knockdown (Fig. S3E).”
Quote in the paperNot a substantial claim - Findingown data
We observed only a small increase in 5mC at HBRs in HNF4A cKO livers.
“Interestingly, we observed only a small increase in 5mC at HBRs in HNF4A cKO livers, suggesting that either recovery of 5mC is slower than 5hmC loss or it does not occur.”
Quote in the paperSubstantial claim - Findingown data
In HEK293T cells, deletion of the two motifs did not have any additional effect over the single deletions.
“Of note, in HEK293T cells, deletion of the two motifs did not have any additional effect over the single deletions, suggesting that the hepatic environment of HepG2 cells may contain additional factors required for this regulation.”
Quote in the paperNot a substantial claim - Findingown data
Hepatocyte-specific HNF4A bound regions gain H3K27ac in hepatocytes compared to hepatoblasts.
“Of note, these hepatocyte-specific HNF4A bound regions also gain H3K27ac (Fig. 4B) in hepatocytes compared to hepatoblasts.”
Quote in the paperSubstantial claim - Findingown data
Knockdown of HNF4A in mouse HPPL cells caused a reduction of Tet3 mRNA expression (p<0.0001) and protein levels.
“Knockdown of HNF4A in mouse HPPL cells (hepatic progenitor cells proliferating on laminin), which are capable of generating hepatocyte and cholangiocytes similar to mouse hepatoblasts, caused a reduction of Tet3 mRNA expression (p<0.0001) and protein levels (Fig. 6B), suggesting that HNF4A regulates Tet3 expression in hepatic cells.”
Quote in the paperSubstantial claim- Rests on an assumption: Mouse HPPL cells are capable of generating hepatocyte and cholangiocytes similar to mouse hepatoblasts.
- Findingcitation
ENCODE ChIP-seq data in HepG2 cells demonstrated a similar HNF4A bound region with active histone modifications between exon 2 and 3 of TET3 in the human genome.
“Furthermore, ENCODE ChIP-seq data in HepG2 cells demonstrated a similar HNF4A bound region with active histone modifications between exon 2 and 3 of TET3 in the human genome (Fig. S6B).”
Quote in the paperNot a substantial claim - Findingown data
PLA on adult and embryonic mouse liver cryosections validated the close association between HNF4A and TET3 in nuclei of hepatoblasts and hepatocytes in vivo.
“Proximity ligation assay (PLA) on adult and embryonic mouse liver cryosections validated the close association between HNF4A and TET3 (Fig. 5F) in nuclei of hepatoblasts and hepatocytes in vivo.”
Quote in the paperSubstantial claim - Findingown data
HNF4A bound regions acquired during differentiation in hepatocytes are enriched for H3K27ac and 5hmC in hepatocytes.
“Finally, HNF4A bound regions acquired during differentiation in hepatocytes are enriched for H3K27ac and 5hmC in hepatocytes.”
Quote in the paperSubstantial claim - Findingown data
Positive and negative control regions (Gapdh and Six1) had no significant changes in H3K27ac levels.
“Positive and negative controls regions (Gapdh and Six1) had no significant changes in H3K27ac levels.”
Quote in the paperNot a substantial claim - Findingown data
The results of HNF4A overexpression increasing mTET3E enhancer activity were confirmed using HepG2 cells endogenously expressing HNF4A.
“We confirmed these results using HepG2 cells endogenously expressing HNF4A (Fig. 6D).”
Quote in the paperSubstantial claim - Findingown data
Luciferase assays with the human region in HEK293T cells with HNF4A overexpression and HepG2 cells with endogenous HNF4A confirmed HNF4A-mediated regulation of TET3.
“Luciferase assays with the human region (332bp) in HEK293T cells with HNF4A overexpression (Fig. S6C), and HepG2 cells with endogenous HNF4A (Fig. S6D) confirmed HNF4A-mediated regulation of TET3.”
Quote in the paperSubstantial claim - Findingown data
The mouse TET3 enhancer contains two HNF4A motifs (HNF4A-1 and HNF4A-2).
“The mouse TET3 enhancer contains two HNF4A motifs (HNF4A-1 and HNF4A-2) (Fig. 6E).”
Quote in the paperSubstantial claim - Findingown data
Regions that lose HNF4A-binding after differentiation (hepatoblast-specific) showed decreased H3K27ac in adult hepatocytes.
“In contrast, regions that lose HNF4A-binding after differentiation (hepatoblast-specific) showed decreased H3K27ac in adult hepatocytes (Fig. S4A).”
Quote in the paperSubstantial claim - Findingown data
HNF4A binding in hepatocytes is almost exclusively associated with active enhancers marked by histone modifications (H3K4me1 and H3K27ac) and DNA hydroxymethylation (5hmC).
“In particular, we show that HNF4A binding in hepatocytes is almost exclusively associated with active enhancers marked by histone modifications (H3K4me1 and H3K27ac) and DNA hydroxymethylation (5hmC), supporting a primary role of HNF4A in transcriptional activation.”
Quote in the paperSubstantial claim - Findingown data
In cKO livers, the same genomic locations exhibited a reduction in 5hmC to the same extent (almost two fold change) for both HNF4A only and HNF4A/FOXA2 shared regions.
“Furthermore, in cKO livers, the same genomic locations exhibited a reduction in 5hmC to the same extent (almost two fold change) for both HNF4A only and HNF4A/FOXA2 shared regions (Fig. 3D).”
Quote in the paperSubstantial claim - Findingown data
Combinatorial deletion of these motifs diminished luciferase activity in HepG2 cells.
“As expected, combinatorial deletion of these motifs diminished luciferase activity in HepG2 cells (Fig. 6F).”
Quote in the paperSubstantial claim - Findingown data
These PLA findings were further validated in HEK293T cells using expression of Myc-HNF4A and Flag-TET3.
“These PLA findings were further validated in HEK293T cells using the expression of Myc-HNF4A and Flag-TET3 (Fig. S5D).”
Quote in the paperNot a substantial claim - Findingown data
HNF4A frequently co-binds to regions with FOXA2.
“For example, HNF4A frequently co-binds to regions with FOXA2; however, at regions that are bound by FOXA2 alone very little H3K27ac is evident.”
Quote in the paperNot a substantial claim - Findingown data
There are 2765 hepatocyte-specific HBRs that are evident in differentiated hepatocytes but not bound in hepatoblasts.
“We identified 2765 hepatocyte-specific HBRs that are evident in differentiated hepatocytes but not bound in hepatoblasts (examples are shown in Fig. 4A).”
Quote in the paperSubstantial claim - Findingown data
In hepatoblasts, there is a strong intragenic HNF4A binding site approximately 19kb downstream from the Tet3 transcriptional start site.
“In hepatoblasts, we observed a strong intragenic HNF4A binding site approximately 19kb downstream from the Tet3 transcriptional start site.”
Quote in the paperSubstantial claim - Findingown data
Loss of HNF4A in adult liver through an inducible knockout model leads to reduced levels of H3K27ac and 5hmC at HNF4A bound regions.
“Moreover, our data suggest that HNF4A is required for the presence of H3K27ac and 5hmC since loss of HNF4A in adult liver, through an inducible knockout model, leads to reduced levels of these marks at HNF4A bound regions.”
Quote in the paperSubstantial claim - Findingown data
HNF4A overexpression significantly increased enhancer activity of mTET3E in HEK293T cells.
“HNF4A overexpression significantly increased (p>0.0001) enhancer activity of mTET3E (Fig. 6C).”
Quote in the paperSubstantial claim - Findingown data
This correlates with less transcription from associated genes.
“This correlates with less transcription from associated genes (Fig. 7).”
Quote in the paperSubstantial claim - Findingown data
At regions bound by FOXA2 alone, very little H3K27ac is evident.
“For example, HNF4A frequently co-binds to regions with FOXA2; however, at regions that are bound by FOXA2 alone very little H3K27ac is evident.”
Quote in the paperSubstantial claim - Findingown data
Significant changes in 5hmC upon HNF4A depletion were observed both in vivo and in vitro.
“By first identifying HNF4A-bound regions, we were able to observe significant changes in 5hmC upon HNF4A depletion both in vivo and in vitro, demonstrating its role in the maintenance of this active mark at enhancers (Fig. 7).”
Quote in the paperSubstantial claim - Findingown data
In HNF4A KO livers, H3K27ac was reduced at regions bound by either HNF4A alone or FOXA2/HNF4A.
“In addition, in HNF4A KO livers, H3K27ac was reduced at regions bound by either HNF4A alone or FOXA2/HNF4A, indicating HNF4A is primarily responsible for maintaining active epigenetic signatures at these locations.”
Quote in the paperSubstantial claim - Findingown data
Loss of HNF4A resulted in decreased H3K27ac at all sites bound by HNF4A and/or FOXA2.
“H3K27ac ChIP-qPCR in WT and cKO livers showed that loss of HNF4A resulted in decreased H3K27ac at all sites, indicating a requirement for HNF4A in ensuring H3K27ac is maintained (Fig. 3C).”
Quote in the paperSubstantial claim - Findingown data
Regions bound by HNF4A specifically in hepatoblasts but not hepatocytes have lower H3K27ac and 5hmC in hepatocytes.
“In addition, regions bound by HNF4A specifically in hepatoblasts but not hepatocytes have lower H3K27ac and 5hmC in hepatocytes.”
Quote in the paperSubstantial claim - Findingown data
TET3 co-immunoprecipitates with HNF4A in HepG2 cells, confirming that the two proteins interact.
“Of note, TET3 co-immunoprecipitation with HNF4A in HepG2 cells, which express high levels of both HNF4A and TET3, confirmed that the two proteins interact (Fig. 5C).”
Quote in the paperSubstantial claim - Findingown data
This HNF4A site co-localizes with histone modifications H3K4me1 and H3K27ac.
“This HNF4A site co-localizes with histone modifications H3K4me1 and H3K27ac, suggesting an active enhancer (Fig. 6A).”
Quote in the paperSubstantial claim - Findingown data
In HNF4A cKO livers, 5hmC was reduced around HBRs.
“In HNF4A cKO livers, 5hmC was reduced around HBRs.”
Quote in the paperSubstantial claim - Findingown data
TET3 is highly expressed in hepatocytes.
“We focused on TET3 due to its high expression in hepatocytes (Fig. 5A and 5B) and its known interactions with another nuclear receptor family member, TRα1 (36).”
Quote in the paperSubstantial claim - Findingown data
The HNF4A-TET3 interaction was confirmed using expression of tagged proteins in HEK293T cells.
“This interaction was also confirmed using expression of tagged proteins in HEK293T cells (Fig.S5B).”
Quote in the paperSubstantial claim - Findingnone given
TET3 is more highly expressed compared to other TETs in liver.
“Here, we focused on TET3 because it is more highly expressed compared to other TETs in liver and is known to interact with other TFs (36).”
Quote in the paperSubstantial claim - Findingown data
Loss of HNF4A in HepG2 produced similar changes in DNA modifications as observed in Hnf4a cKO mouse livers.
“We also confirmed that loss of HNF4A in a human hepatoma cell line, HepG2, produced similar changes in DNA modifications as observed in Hnf4a cKO mouse livers, indicating similar mechanisms of gene regulation (Fig. S3 and Fig. 7).”
Quote in the paperSubstantial claim - Findingreasoning
HBRs are associated with a high level of H3K27ac and 5hmC.
“In summary, we show that HBRs are associated with a high level of H3K27ac and 5hmC, likely due to HNF4A interactions with CBP/p300 and TET3 respectively (Fig. 7).”
Quote in the paperSubstantial claim - Interpretationown data
HNF4A-mediated oxidation of 5mC to 5hmC during differentiation of hepatoblasts to hepatocytes is achieved by its interaction with TET3, a newly identified HNF4A target gene in hepatoblasts.
“Furthermore, HNF4A-mediated oxidation of 5mC to 5hmC during differentiation of hepatoblasts to hepatocytes is achieved by its interaction with TET3, a newly identified HNF4A target gene in hepatoblasts.”
Quote in the paperSubstantial claim- Rests on an assumption: 5hmC is produced by oxidation of 5mC due to activity of TET1, TET2 and TET3.
- Interpretationown data
Loss of HNF4A during liver differentiation confirms that HNF4A is required for establishment and maintenance of H3K27ac.
“Loss of HNF4A during liver differentiation confirmed that HNF4A is required for establishment and maintenance of H3K27ac.”
Quote in the paperSubstantial claim - Interpretationown data
HNF4A is required for the active epigenetic state at enhancers that amplifies transcription of genes in hepatocytes.
“In conclusion, we identified that HNF4A is required for the active epigenetic state at enhancers that amplifies transcription of genes in hepatocytes.”
Quote in the paperSubstantial claim - Interpretationown data
HNF4A-associated 5hmC requires its interaction with TET3, a protein responsible for oxidation from 5mC to 5hmC.
“Mechanistically, HNF4A-associated hydroxymethylation (5hmC) requires its interaction with TET3, a protein responsible for oxidation from 5mC to 5hmC.”
Quote in the paperSubstantial claim- Rests on an assumption: 5hmC is produced by oxidation of 5mC due to activity of TET1, TET2 and TET3.
- Interpretationown data
HNF4A-driven epigenetic changes are required for expression of target genes during hepatocyte differentiation.
“Overall, we confirm that HNF4A-driven epigenetic changes are required for expression of target genes during hepatocyte differentiation.”
Quote in the paperSubstantial claim - Premisecitation
HNF4A deficiency in mouse embryonic liver causes failure in hepatocyte differentiation.
“HNF4A deficiency in mouse embryonic liver causes failure in hepatocyte differentiation (2), while in adult mice loss of HNF4A affects lipid homeostasis leading to liver steatosis (5).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [2] Li J, Ning G, Duncan SA. Mammalian hepatocyte differentiation requires the transcription factor HNF-4alpha. Genes Dev. 2000; 14: 464– 474. 10691738 PMC316377
- Interpretationown data
HNF4A is required for the presence of H3K27ac and 5hmC.
“Moreover, our data suggest that HNF4A is required for the presence of H3K27ac and 5hmC since loss of HNF4A in adult liver, through an inducible knockout model, leads to reduced levels of these marks at HNF4A bound regions.”
Quote in the paperSubstantial claim - Interpretationown data
HNF4A regulates Tet3 expression in hepatic cells.
“Knockdown of HNF4A in mouse HPPL cells (hepatic progenitor cells proliferating on laminin), which are capable of generating hepatocyte and cholangiocytes similar to mouse hepatoblasts, caused a reduction of Tet3 mRNA expression (p<0.0001) and protein levels (Fig. 6B), suggesting that HNF4A regulates Tet3 expression in hepatic cells.”
Quote in the paperSubstantial claim- Rests on an assumption: Mouse HPPL cells are capable of generating hepatocyte and cholangiocytes similar to mouse hepatoblasts.
- Interpretationown data
HNF4A functions to regulate DNA methylation in the surrounding genomic regions through interactions with TET3.
“In the present study, we show that HNF4A functions to regulate DNA methylation in the surrounding genomic regions through interactions with TET3.”
Quote in the paperSubstantial claim - Interpretationown data
HNF4A has a primary role in transcriptional activation.
“In particular, we show that HNF4A binding in hepatocytes is almost exclusively associated with active enhancers marked by histone modifications (H3K4me1 and H3K27ac) and DNA hydroxymethylation (5hmC), supporting a primary role of HNF4A in transcriptional activation.”
Quote in the paperSubstantial claim - Interpretationown data
HNF4A interacts with TET3 to mediate the active 5hmC status.
“Together, our findings suggest that HNF4A physically interacts with TET3, in vitro and in vivo, to mediate the active 5hmC status and that presence of both are required for expression of genes associated with HBRs.”
Quote in the paperSubstantial claim - Interpretationown data
Addition of HNF4A in hepatocyte-specific HBRs results in oxidation of 5mC to 5hmC.
“Moreover, hepatocyte-specific HBRs show decreased levels of 5mC (Fig. 4C) and increased levels of 5hmC (Fig. 4D) in hepatocytes compared to hepatoblasts, suggesting that addition of HNF4A in those regions results in oxidation of 5mC to 5hmC.”
Quote in the paperSubstantial claim- Rests on an assumption: 5hmC is produced by oxidation of 5mC due to activity of TET1, TET2 and TET3.
- Interpretationown data
HNF4A directly regulates Tet3 in hepatic cells.
“Overall, our results suggest that HNF4A directly regulates Tet3 in hepatic cells and TET3 interacts with HNF4A to control the epigenetic environment by ensuring 5hmC and H3K27ac are maintained.”
Quote in the paperSubstantial claim- Rests on an assumption: Mouse HPPL cells are capable of generating hepatocyte and cholangiocytes similar to mouse hepatoblasts.
- Interpretationown data
HNF4A is a facilitator of the active enhancer state.
“Together this data establishes HNF4A as a facilitator of the active enhancer state.”
Quote in the paperSubstantial claim - Interpretationown data
HNF4A is primarily responsible for maintaining active epigenetic signatures at these locations.
“In addition, in HNF4A KO livers, H3K27ac was reduced at regions bound by either HNF4A alone or FOXA2/HNF4A, indicating HNF4A is primarily responsible for maintaining active epigenetic signatures at these locations.”
Quote in the paperSubstantial claim - Interpretationown data
This HNF4A site suggests an active enhancer.
“This HNF4A site co-localizes with histone modifications H3K4me1 and H3K27ac, suggesting an active enhancer (Fig. 6A).”
Quote in the paperSubstantial claim - Interpretationown data
HNF4A has a role in the maintenance of 5hmC at enhancers.
“By first identifying HNF4A-bound regions, we were able to observe significant changes in 5hmC upon HNF4A depletion both in vivo and in vitro, demonstrating its role in the maintenance of this active mark at enhancers (Fig. 7).”
Quote in the paperSubstantial claim - Premisecitation
HNF4A directly interacts with CBP/p300.
“HNF4A was shown to directly interact with CBP/p300, which may account for its ability to regulate H3K27ac (2, 41, 42).”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [2] Li J, Ning G, Duncan SA. Mammalian hepatocyte differentiation requires the transcription factor HNF-4alpha. Genes Dev. 2000; 14: 464– 474. 10691738 PMC316377
- cites [41] Yoshida E, Aratani S, Itou H, Miyagishi M, Takiguchi M, Osumu T, Functional Association between CBP and HNF4 inTrans-activation. Biochem. Biophys. Res. Commun. 1997; 241: 664– 669. 9434765 source
- cites [42] Eeckhoute J, Formstecher P, Laine B. Hepatocyte nuclear factor 4alpha enhances the hepatocyte nuclear factor 1alpha-mediated activation of transcription. Nucleic Acids Res. 2004; 32: 2586– 93. 15141028 PMC419469 source
- Interpretationown data
TET3 interacts with HNF4A to control the epigenetic environment by ensuring 5hmC and H3K27ac are maintained.
“Overall, our results suggest that HNF4A directly regulates Tet3 in hepatic cells and TET3 interacts with HNF4A to control the epigenetic environment by ensuring 5hmC and H3K27ac are maintained.”
Quote in the paperSubstantial claim - Interpretationcitation
Changes in 5mC upon HNF4A depletion in the whole liver may be difficult to observe.
“Furthermore, it has previously been shown that 5hmC abundance represents only ~10% of the 5mC level in embryonic stem cells,(45), thus changes in 5mC upon HNF4A depletion in the whole liver may be difficult to observe.”
Quote in the paperNot a substantial claim - Interpretationown data
HNF4A is required to maintain high levels of H3K27ac and 5hmC in vivo and in cell lines.
“Together, these findings suggest that HNF4A is required to maintain high levels of H3K27ac and 5hmC in in vivo and cell lines.”
Quote in the paperSubstantial claim - Interpretationcitation
HNF4A's interaction with CBP/p300 may account for its ability to regulate H3K27ac.
“HNF4A was shown to directly interact with CBP/p300, which may account for its ability to regulate H3K27ac (2, 41, 42).”
Quote in the paperNot a substantial claim - Interpretationown data
HNF4A controls gene expression through its influence on epigenetic modifications in hepatoblasts and hepatocytes.
“Here, we show that HNF4A, a master regulator of hepatocyte differentiation, controls gene expression through its influence on epigenetic modifications in hepatoblasts and hepatocytes.”
Quote in the paperSubstantial claim- Rests on an assumption: The role of HNF4A in epigenetic-mediated gene regulation in liver is not well defined.
- Interpretationreasoning
Presence of both HNF4A and TET3 are required for expression of genes associated with HBRs.
“Together, our findings suggest that HNF4A physically interacts with TET3, in vitro and in vivo, to mediate the active 5hmC status and that presence of both are required for expression of genes associated with HBRs.”
Quote in the paperSubstantial claim - Interpretationown data
HNF4A regulates epigenetic plasticity in hepatic cells.
“Thus, we have identified a mechanism through which HNF4A regulates epigenetic plasticity in hepatic cells.”
Quote in the paperSubstantial claim - Interpretationown data
This function can be independent of FOXA2.
“We have also confirmed HNF4A function in establishment and maintenance of H3K27ac and 5hmC at enhancers and that this function can be independent of FOXA2.”
Quote in the paperSubstantial claim - Interpretationown data
This indicates similar mechanisms of gene regulation.
“We also confirmed that loss of HNF4A in a human hepatoma cell line, HepG2, produced similar changes in DNA modifications as observed in Hnf4a cKO mouse livers, indicating similar mechanisms of gene regulation (Fig. S3 and Fig. 7).”
Quote in the paperSubstantial claim - Interpretationown data
HNF4A functions in establishment and maintenance of H3K27ac and 5hmC at enhancers.
“We have also confirmed HNF4A function in establishment and maintenance of H3K27ac and 5hmC at enhancers and that this function can be independent of FOXA2.”
Quote in the paperSubstantial claim
- Classified as probably not a substantial claim. 30
- May combine two claims. 32
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationA recent study showed that HNF4A loss can impact global 5mC and 5hmC to a small extent.
“A recent study showed that HNF4A loss can impact global 5mC and 5hmC to a small extent (44).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [44] Zhang Q, Lei X, Lu H. Alterations of Epigenetic Signatures in Hepatocyte Nuclear Factor 4a Deficient Mouse Liver Determined by Improved ChIP-qPCR and (h)MeDIP-qPCR Assays. 2014; PMC3888413 24427299 source
The Results section on DNA methylation and 5-hydroxymethylation (page unavailable) reports no significant difference in total immunoprecipitated DNA fragments between Hnf4a-deficient and wild-type livers. The Discussion explicitly says Hnf4a deficiency does not cause global changes in DNA methylation or 5-hydroxymethylation; it finds changes at specific gene loci instead. (LLM, conf=0.90)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationEctopic HNF4A expression in fibroblasts induces DNase1 hypersensitivity of the Serpin gene cluster at 14q32.1 to transcriptionally regulate α1-antitrypsin and corticosteroid binding globulin.
“Previous studies have suggested that HNF4A plays multiple roles in chromatin reorganization: ectopic HNF4A expression in fibroblasts was shown to induce DNase1 hypersensitivity of the Serpin gene cluster at 14q32.1 to transcriptionally regulate α1-antitrypsin and corticosteroid binding globulin (39).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [39] Rollini P, Fournier RE. The HNF-4/HNF-1alpha transactivation cascade regulates gene activity and chromatin structure of the human serine protease inhibitor gene cluster at 14q32.1. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 10308– 13. 10468604 PMC17884 source
The Results report that HNF-4 expression induced DNase I-hypersensitive sites and rescued α1-antitrypsin and CBG expression in transactivator-deficient hepatoma hybrids, not fibroblasts. The Discussion explicitly says that rat fibroblast α1-antitrypsin genes are refractory to activation by HNF-4, contrary to the claimed fibroblast result. (LLM, conf=0.88)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationHNF4A binding is highly dynamic and bound regions can change based on tissue and differentiation state.
“We have shown that HNF4A binding is highly dynamic and that bound regions can change based on tissue and differentiation state (11).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [11] Alder O, Cullum R, Lee S, Kan AC, Wei W, Yi Y, Hippo signaling influences HNF4A and FOXA2 enhancer switching during hepatocyte differentiation. Cell Rep. 2014; 9: 261– 271. 25263553 PMC4612615 source
In Results, under “HNF4A and FOXA2 Bind the Genome in a Differentiation-Dependent Manner” (page unavailable), the paper reports that 55% of HNF4A-binding sites were occupied uniquely in either embryonic or adult liver. This supports dynamic binding across differentiation states, but the passages do not establish that HNF4A-bound regions change between different tissues. (LLM, conf=0.86)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Premisecitation5hmC plays an important role during mammalian development and cellular differentiation; Tet1/2/3 deficiency in ES cells reduces differentiation capabilities and limits developmental potential during embryogenesis.
“5hmC plays an important role during mammalian development and cellular differentiation: Tet½/3 deficiency in ES cells (triple knockout cells) reduces their differentiation capabilities and also limits their developmental potential during embryogenesis (19).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [19] Dawlaty MM, Breiling A, Le T, Barrasa MI, Raddatz G, Gao Q, Loss of Tet enzymes compromises proper differentiation of embryonic stem cells. Dev. Cell. 2014; 29: 102– 11. 24735881 PMC4035811 source
May combine two claims.
Findingown dataK-means clustering (K=5) on HNF4A and FOXA2 bound regions identified 5 clusters, with large overlap between HBRs and FBRs (Cl2, Cl3, Cl4) and two clusters showing exclusive binding of either HNF4A or FOXA2 (Cl1 and Cl5).
“To address this, we performed K-means clustering (K=5) on HNF4A and FOXA2 bound regions in hepatocytes using ChAsE (35) and identified 5 clusters. As expected, a large overlap was observed between HBRs and FBRs (Cl2, Cl3 and Cl4), however, two clusters showed exclusive binding of either HNF4A or FOXA2 (Cl1 and Cl5, respectively) (Fig. 2A).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [35] Younesy H, Nielsen CB, Lorincz MC, Jones SJM, Karimi MM, Möller T. ChAsE: chromatin analysis and exploration tool. Bioinformatics. 2016; 32: 3324– 3326. 27378294 PMC5079470 source
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationIn liver, HNF4A is required for normal development, including morphogenesis and differentiation, and controls other TFs critical in liver cell fate as well as genes necessary for hepatocyte functions.
“In liver, HNF4A is required for normal development (2), including morphogenesis (3) and differentiation (4), and controls other TFs critical in liver cell fate as well as genes necessary for hepatocyte functions.”
Quote in the paperNot a substantial claim1 of 3 sources checked- cites [2] Li J, Ning G, Duncan SA. Mammalian hepatocyte differentiation requires the transcription factor HNF-4alpha. Genes Dev. 2000; 14: 464– 474. 10691738 PMC316377
- cites [3] DeLaForest A, Nagaoka M, Si-Tayeb K, Noto FK, Konopka G, Battle MA, HNF4A is essential for specification of hepatic progenitors from human pluripotent stem cells. Development. 2011; 138: 4143– 53. 21852396 PMC3171218 source
- cites [4] Bonzo JA, Ferry CH, Matsubara T, Kim J-H, Gonzalez FJ. Suppression of Hepatocyte Proliferation by Hepatocyte Nuclear Factor 4α in Adult Mice. J. Biol. Chem. 2012; 287: 7345– 7356. 22241473 PMC3293558 source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationHNF4A is expressed in the liver, pancreas, gastrointestinal tract and kidneys.
“Hepatocyte nuclear factor 4A (HNF4A, also known as NR2A1) is a member of the nuclear receptor superfamily of transcription factors (TFs) and is expressed in the liver, pancreas, gastrointestinal tract and kidneys (1).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [1] Sladek FM, Zhong WM, Lai E, Darnell JE. Liver-enriched transcription factor HNF-4 is a novel member of the steroid hormone receptor superfamily. Genes Dev. 1990; 4: 2353– 65. 2279702 source
The section “Tissue distribution of HNF-4 mRNA is limited” reports HNF-4 mRNA in rat liver, kidney, and intestine, supporting those parts of the claim. It does not report expression in the pancreas, and intestine is narrower than the gastrointestinal tract as a whole. (LLM, conf=0.89)
Experimental — accuracy not yet measured
Classified as probably not a substantial claim. May combine two claims.
PremisecitationActive cis-regulatory regions are located in open chromatin regions, while condensed chromatin is inaccessible and inactive.
“Genome-wide epigenetic analysis has proven that active cis-regulatory regions are located in open chromatin regions (12), while condensed chromatin is inaccessible and thus inactive.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [12] Mueller B, Mieczkowski J, Kundu S, Wang P, Sadreyev R, Tolstorukov MY, Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction. Genes Dev. 2017; 31: 451– 462. 28356342 PMC5393060 source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationGenome-wide enrichment studies in human and mouse ESCs confirm the presence of 5hmC at promoters and enhancers in addition to gene bodies.
“Genome-wide enrichment studies in human and mouse embryonic stem cells (ESCs) confirms the presence of 5hmC at promoters and enhancers in addition to gene bodies (20).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [20] Pastor WA, Pape UJ, Huang Y, Henderson HR, Lister R, Ko M, Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature. 2011; 473: 394– 397. 21552279 PMC3124347 source
The paper reports genome-wide mapping in mouse embryonic stem cells and finds 5hmC in transcribed regions, at transcription start sites and promoters, and in enhancers (Abstract; no page supplied). The cited study does not establish these findings in human embryonic stem cells, so the claim's inclusion of human cells is unsupported by this source. (LLM, conf=0.88)
Experimental — accuracy not yet measured
Classified as probably not a substantial claim. May combine two claims.
PremisecitationH3K4me1 and H3K4me3 mark enhancers and promoters respectively.
“In particular, lysine 4 of histone 3 monomethylation (H3K4me1) and trimethylation (H3K4me3) mark enhancers and promoters respectively (15).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [15] Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res. 2008; 18: 1906– 1917. 18787082 PMC2593584 source
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationHNF4A is crucial for generating induced hepatocyte-like cells (iHeps), and HNF4A overexpression alone may be sufficient to generate these cells.
“These studies revealed that HNF4A is crucial for generating induced hepatocyte-like cells (iHeps) (25, 26) as HNF4A overexpression alone may be sufficient to generate these cells (27).”
Quote in the paperNot a substantial claim1 of 3 sources checked- cites [25] Huang P, He Z, Ji S, Sun H, Xiang D, Liu C, Induction of functional hepatocyte-like cells from mouse fibroblasts by defined factors. Nature. 2011; 475: 386– 389. 21562492 source
- cites [26] Sekiya S, Suzuki A. Direct conversion of mouse fibroblasts to hepatocyte-like cells by defined factors. Nature. 2011; 475: 390– 393. 21716291 source
- cites [27] Nakamori D, Akamine H, Takayama K, Sakurai F, Mizuguchi H. Direct conversion of human fibroblasts into hepatocyte-like cells by ATF5, PROX1, FOXA2, FOXA3, and HNF4A transduction. Sci. Rep. 2017; 7: 16675. 29192290 PMC5709502 source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationRecent reports have identified TFs that interact with TET proteins to maintain low 5mC and high 5hmC at enhancers.
“Recent reports have identified TFs that interact with TET proteins to maintain low 5mC and high 5hmC at enhancers (23, 24).”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [23] Fujiki K, Shinoda A, Kano F, Sato R, Shirahige K, Murata M. PPARγ-induced PARylation promotes local DNA demethylation by production of 5-hydroxymethylcytosine. Nat. Commun. 2013; 4: 2262. 23912449 source
The section on Tet-mediated hydroxylation reports that PPARγ associates with Tet1 and promotes demethylation and 5hmC production around PPREs; the Discussion identifies the Plin1 PPRE as an adipogenic enhancer. But the paper describes a transient rise in 5hmC during differentiation, followed by a decline, rather than maintenance of high 5hmC at enhancers. (LLM, conf=0.85)
Experimental — accuracy not yet measured - cites [24] Yang YA, Zhao JC, Fong K-W, Kim J, Li S, Song C, FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function. Nucleic Acids Res. 2016; 44: 8153– 64. 27257062 PMC5041455 source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationH3K27ac is associated with the active state of both enhancers and promoters.
“In addition, acetylation of lysine 27 of histone 3 (H3K27ac) is associated with the active state of both elements.”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [13] Zhu H, Wang G, Qian J. Transcription factors as readers and effectors of DNA methylation. Nat. Rev. Genet. 2016; 17: 551– 565. 27479905 PMC5559737 source
The Cis-regulatory elements section (page unavailable) describes H3K27ac as an active mark in enhancers, supporting the enhancer part of the claim. It does not link H3K27ac to active promoters, so the claim about both elements is only partially supported. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [14] Calo E, Wysocka J. Modification of enhancer chromatin: what, how and why? 2013; Mol Cell. 2013; 49: 825– 837 23473601 PMC3857148 source
Classified as probably not a substantial claim.
PremisecitationThe establishment and maintenance of patterns of histone and DNA modifications in a tissue-specific manner may be controlled by TFs directly or indirectly interacting with epigenetic modifiers, such as the histone acetylase CBP/p300.
“The establishment and maintenance of patterns of histone and DNA modifications in a tissue-specific manner may be controlled by TFs directly or indirectly interacting with epigenetic modifiers (21), such as the histone acetylase CBP/p300 (22).”
Quote in the paperSubstantial claim2 of 2 sources checked- cites [21] Perera A, Eisen D, Wagner M, Laube SK, Künzel AF, Koch S, TET3 Is Recruited by REST for Context-Specific Hydroxymethylation and Induction of Gene Expression. Cell Rep. 2015; 11: 283– 294. 25843715 source
- cites [22] Choi SH, Gearhart MD, Cui Z, Bosnakovski D, Kim M, Schennum N, DUX4 recruits p300/CBP through its C-terminus and induces global H3K27 acetylation changes. Nucleic Acids Res. 2016; 44: 5161– 5173. 26951377 PMC4914088 source
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Premisecitation5mC is associated with gene repression and can disrupt the binding of many TFs.
“DNA methylation (5-methylcytosine or 5mC) is associated with gene repression (16) and can disrupt the binding of many TFs (17, 18).”
Quote in the paperNot a substantial claim2 of 3 sources checked- cites [16] Boyes J, Bird A. Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein. EMBO J. 1992; 11: 327– 33. 1310933 PMC556453 source
- cites [17] Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science (80-.). 2017; 356: eaaj2239. PMC8009048 28473536 source
- cites [18] Schübeler D, Lorincz MC, Cimbora DM, Telling A, Feng YQ, Bouhassira EE, Genomic targeting of methylated DNA: influence of methylation on transcription, replication, chromatin structure, and histone acetylation. Mol. Cell. Biol. 2000; 20: 9103– 12. 11094062 PMC102168 source
May combine two claims.
PremisecitationThe HNF4A binding motif does not contain a CG which can be methylated, thus making it a methylation-insensitive TF.
“Of interest, the HNF4A binding motif does not contain a CG which can be methylated, thus making it a methylation-insensitive TF (11, 17).”
Quote in the paperSubstantial claim2 of 2 sources checked- cites [11] Alder O, Cullum R, Lee S, Kan AC, Wei W, Yi Y, Hippo signaling influences HNF4A and FOXA2 enhancer switching during hepatocyte differentiation. Cell Rep. 2014; 9: 261– 271. 25263553 PMC4612615 source
The Results section on motif analysis (page unavailable) compares HNF4A motifs across developmental stages but does not say whether the motif contains a CG or whether HNF4A binding is insensitive to DNA methylation. Searches for those specific points found no supporting passage in our copy. (LLM, conf=0.72)
Experimental — accuracy not yet measured - cites [17] Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science (80-.). 2017; 356: eaaj2239. PMC8009048 28473536 source
The sections “CpG methylation has a major effect on TF-DNA binding” and “Binding of most TFs can be affected by CpG methylation” say that TFs whose recognition sequences lack CpG are not affected by CpG methylation. Our copy does not identify HNF4A as one of those TFs or establish that its binding motif lacks CG, so the HNF4A-specific claim is not verified. (LLM, conf=0.82)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationA previous study observed a similar effect at FOXA1 bound enhancers in LNCaP prostate cancer cells in which knockdown of FOXA1 reduced 5hmC without gain of 5mC.
“A previous study observed a similar effect at FOXA1 bound enhancers in LNCaP prostate cancer cells in which knockdown of FOXA1 reduced 5hmC without gain of 5mC (24).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [24] Yang YA, Zhao JC, Fong K-W, Kim J, Li S, Song C, FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function. Nucleic Acids Res. 2016; 44: 8153– 64. 27257062 PMC5041455 source
In Results (‘FOXA1 expression contributes to lineage-specific enhancer activation’), FOXA1 knockdown in LNCaP cells significantly decreased 5hmC at FOXA1-binding sites, while average 5mC intensity was not substantially affected. The same passage reports moderate 5mC increases at individual sites by MeDIP-PCR (Supplementary Figure S3), so ‘without gain of 5mC’ is supported at the genome-wide level but not without qualification. (LLM, conf=0.89)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationTET3 has known interactions with another nuclear receptor family member, TRα1.
“We focused on TET3 due to its high expression in hepatocytes (Fig. 5A and 5B) and its known interactions with another nuclear receptor family member, TRα1 (36).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [36] Guan W, Guyot R, Samarut J, Flamant F, Wong J, Gauthier KC. Methylcytosine dioxygenase TET3 interacts with thyroid hormone nuclear receptors and stabilizes their association to chromatin. Proc. Natl. Acad. Sci. U. S. A. 2017; 114: 8229– 8234. 28716910 PMC5547603 source
Classified as probably not a substantial claim.
Premisecitation5hmC abundance represents only ~10% of the 5mC level in embryonic stem cells.
“Furthermore, it has previously been shown that 5hmC abundance represents only ~10% of the 5mC level in embryonic stem cells,(45), thus changes in 5mC upon HNF4A depletion in the whole liver may be difficult to observe.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [45] Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009; 324: 930– 5. 19372391 PMC2715015 source
The passage describing Fig. 5A reports that 5hmC and 5mC account for 4–6% and 55–60%, respectively, of cytosines at MspI cleavage sites in mouse embryonic stem cells—a ratio of roughly 10%. The measurement is limited to those sites, so it does not establish that ratio for all DNA in embryonic stem cells. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationHNF4A was previously shown to recruit several coactivators such as glucocorticoid receptor interacting protein 1, steroid receptor coactivator1 and cAMP response element binding proteins to regulate gene expression.
“In addition to FOXA family members, HNF4A was previously shown to recruit several coactivators such as glucocorticoid receptor interacting protein 1, steroid receptor coactivator1 and cAMP response element binding proteins to regulate gene expression (41, 43).”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites [41] Yoshida E, Aratani S, Itou H, Miyagishi M, Takiguchi M, Osumu T, Functional Association between CBP and HNF4 inTrans-activation. Biochem. Biophys. Res. Commun. 1997; 241: 664– 669. 9434765 source
- cites [43] Wang J-C, Stafford JM, Granner DK. SRC-1 and GRIP1 coactivate transcription with hepatocyte nuclear factor 4. J. Biol. Chem. 1998; 273: 30847– 30850. 9812974 PMC3968904 source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationTET3 is known to interact with other TFs.
“Here, we focused on TET3 because it is more highly expressed compared to other TETs in liver and is known to interact with other TFs (36).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [36] Guan W, Guyot R, Samarut J, Flamant F, Wong J, Gauthier KC. Methylcytosine dioxygenase TET3 interacts with thyroid hormone nuclear receptors and stabilizes their association to chromatin. Proc. Natl. Acad. Sci. U. S. A. 2017; 114: 8229– 8234. 28716910 PMC5547603 source
Classified as probably not a substantial claim.
PremisecitationTET2 and TET3 are known to be required for this 5mC oxidation process in hepatocytes.
“TET2 and TET3 are known to be required for this 5mC oxidation process in hepatocytes (46).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [46] Reizel Y, Sabag O, Skversky Y, Spiro A, Steinberg B, Bernstein D, Postnatal DNA demethylation and its role in tissue maturation. Nat. Commun. 2018; 9: 2040. 29795194 PMC5966414 source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationTET3 can identify and facilitate removal of 5caC by base excision repair to achieve demethylation of gene regulatory regions.
“A recent study showed that TET3 can identify and facilitate removal of 5caC by base excision repair to achieve demethylation of gene regulatory regions (47).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [47] Jin S-G, Zhang Z-M, Dunwell TL, Harter MR, Wu X, Johnson J, Tet3 Reads 5-Carboxylcytosine through Its CXXC Domain and Is a Potential Guardian against Neurodegeneration. Cell Rep. 2016; 14: 493– 505. 26774490 PMC4731272 source
The Results (DNA binding properties; page not provided) show that Tet3’s CXXC domain recognizes 5caC. The Discussion (page not provided) proposes that Tet3FL may promote expression of base-excision-repair factors, but does not establish that it facilitates 5caC removal or demethylation at gene regulatory regions. The Results also found no effect of Tet3’s CXXC domain on TDG cleavage of 5caC. (LLM, conf=0.88)
Experimental — accuracy not yet measured
May combine two claims.
Findingown dataMotif analysis of cluster 5 revealed high enrichment for the FOXA2 motif and low enrichment for NFIC and CTCF.
“In contrast, motif analysis of cluster 5 revealed high enrichment for the FOXA2 motif and low enrichment for NFIC and CTCF (Fig. S2C).”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThere is low but significant enrichment of HNF4A motifs in cluster 5, where HNF4A ChIP-seq data confirmed no binding in hepatocytes.
“Interestingly, we also observed low, but significant, enrichment of HNF4A motifs in cluster 5, where our HNF4A ChIP-seq data confirmed no binding in hepatocytes.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataCl5 regions show decreased H3K4me1, H3K27ac and 5hmC but increased 5mC compared to regions with HNF4A bound.
“These show decreased levels of H3K4me1 (Fig. 2B), H3K27ac (Fig. 2C) and 5hmC (Fig. 2D) but an increase in 5mC (Fig. 2E) at regions in Cl5, which do not have HNF4A bound.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Findingown dataCluster 1 genes are frequently associated with metabolic functions and cluster 5 genes are associated with various signaling pathways.
“Gene classification analysis to highlight the functions of genes associated with these clusters showed that cluster 1 genes are frequently associated with metabolic functions (Fig. S2D) and cluster 5 genes are associated with various signaling pathways (Fig. S2E).”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataHNF4A occupies active enhancers in hepatocytes and is essential for active histone and DNA signatures, especially H3K27ac and 5hmC.
“Using analysis of genome-wide histone modifications, DNA methylation and hydroxymethylation in mouse hepatocytes, we show that HNF4A occupies active enhancers in hepatocytes and is essential for active histone and DNA signatures, especially H3K27ac and 5-hydroxymethylcytosine (5hmC).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThere is no significant difference in CpG density between clusters, indicating that 5mC enrichment in Cl5 is independent of CpG density.
“Given the importance of CpG density and its impact on 5mC, we performed CpG density analysis and found no significant difference between clusters, indicating 5mC enrichment in Cl5 is independent of CpG density (data not shown).”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataHBRs are surrounded by high regions of 5hmC but not 5mC.
“We observed that HBRs are surrounded by high regions of 5hmC but not 5mC (Fig. 1A) as illustrated by the combined profile plot (Fig. 1B).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataAnalysis of regions in Cl1 confirmed no enrichment of motifs for FOXA, suggesting no contribution of FOXA family members in maintaining a transcriptional permissive state at those regions.
“Analysis of regions in Cl1 confirmed no enrichment of motifs for FOXA, suggesting no contribution of FOXA family members in maintaining a transcriptional permissive state at those regions (Fig. S2B).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataGenes associated with HNF4A bound regions gained in hepatocytes were significantly more highly expressed in hepatocytes compared to hepatoblasts, whereas genes associated with regions no longer bound by HNF4A in hepatocytes showed the opposite trend.
“Notably, genes associated with HNF4A bound regions gained in hepatocytes were significantly more highly expressed in hepatocytes compared to hepatoblasts (individual and global examples are shown in Fig. 4E and 4F), whereas genes associated with regions no longer bound by HNF4A in hepatocytes showed the opposite trend (Fig. S4B).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataAfter siRNA depletion of HNF4A, these sites had significantly decreased levels of 5hmC and increased levels of 5mC.
“After siRNA depletion of HNF4A, these sites had significantly decreased levels of 5hmC (Fig. S3D) and increased levels of 5mC (Fig. S3E).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThere is an increase in 5mC levels in cKO livers at most loci examined, especially at sites bound only by HNF4A.
“We also observed an increase in 5mC levels in cKO livers at most loci examined (Fig. S3A), especially at those sites that are bound only by HNF4A.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataHepatocyte-specific HBRs show decreased levels of 5mC and increased levels of 5hmC in hepatocytes compared to hepatoblasts.
“Moreover, hepatocyte-specific HBRs show decreased levels of 5mC (Fig. 4C) and increased levels of 5hmC (Fig. 4D) in hepatocytes compared to hepatoblasts, suggesting that addition of HNF4A in those regions results in oxidation of 5mC to 5hmC.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataWe observed depletion of 5mC and enrichment of 5hmC around HNF4 bound regions.
“In addition to H3K27ac, we observed depletion of 5mC and enrichment of 5hmC around HNF4 bound regions.”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationown dataHNF4A maintains an active epigenetic state at cis-regulatory elements in hepatocytes and during liver differentiation.
“Here, we show that HNF4A maintains an active epigenetic state at cis-regulatory elements in hepatocytes and during liver differentiation.”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationown dataHBRs are enriched for H3K4me1 and H3K27ac, DNaseI hypersensitivity and 5hmC, indicating that HNF4A is primarily bound at active enhancers in hepatocytes.
“Overall, our data show that HBRs are enriched for H3K4me1 and H3K27ac, DNaseI hyper-sensitivity and 5hmC, which together indicate that HNF4A is primarily bound at active enhancers in hepatocytes.”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationown dataHNF4A physically interacts with TET3 in vitro and in vivo.
“Together, our findings suggest that HNF4A physically interacts with TET3, in vitro and in vivo, to mediate the active 5hmC status and that presence of both are required for expression of genes associated with HBRs.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S1 (asserted), S3 (load-bearing), S4 (based).
Interpretationnone givenHNF4A, with or without other factors, could have a protective effect that disallows histone deacetylases to act.
“Alternatively, HNF4A, with or without other factors, could have a protective effect that disallows histone deacetylases to act.”
Quote in the paperNot a substantial claimMay combine two claims.
Interpretationown dataIn the absence of HNF4A, histone acetylases either are not recruited or not able to function at HNF4A enhancers, despite the potential presence of other TF binding.
“Our data suggest that in the absence of HNF4A, histone acetylases either are not recruited or not able to function at HNF4A enhancers, despite the potential presence of other TF binding.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductnone givenStudent's t-test was used for qPCR data with GraphPad software, and a p-value <0.05 was considered statistically significant.
“Student’s t-test was used for qPCR data with GraphPad software. A p-value <0.05 was considered statistically significant.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Interpretationown dataH3K27ac at HNF4A binding sites could be affected by interactions with other TFs.
“Thus, H3K27ac at HNF4A binding sites could be affected by interactions with other TFs.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductnone givenThe HNF4A conditional knockout animals were housed at NIH and procedures were carried out in accordance with the Institute of Laboratory Animal Resources guidelines and approved by the National Cancer Institute Animal Care and Use Committee.
“The HNF4A conditional knockout animals were housed at NIH and procedures were carried out in accordance with the Institute of Laboratory Animal Resources guidelines and approved by the National Cancer Institute Animal Care and Use Committee.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenMouse protocols were approved by the University of British Columbia Animal Care committee.
“Mouse protocols were approved by the University of British Columbia Animal Care committee.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenResults are calculated as mean ±SEM derived from at least three independent experiments.
“Results are calculated as mean ±SEM derived from at least three independent experiments.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Interpretationown dataThe hepatic environment of HepG2 cells may contain additional factors required for this regulation.
“Of note, in HEK293T cells, deletion of the two motifs did not have any additional effect over the single deletions, suggesting that the hepatic environment of HepG2 cells may contain additional factors required for this regulation.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Interpretationown dataRecovery of 5mC is slower than 5hmC loss or it does not occur.
“Interestingly, we observed only a small increase in 5mC at HBRs in HNF4A cKO livers, suggesting that either recovery of 5mC is slower than 5hmC loss or it does not occur.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningHNF4A may bind to its motif and then recruit TET proteins to oxidize 5mC to 5hmC in surrounding regions.
“Thus, HNF4A may bind to its motif and then recruit TET proteins to oxidize 5mC to 5hmC in surrounding regions.”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationown dataAt these regions, HNF4A, but not FOXA2, is necessary for the active epigenetic state.
“After examining the data for patterns (Fig. 2A) and how H3K27Ac and 5hmC levels vary, we identified that at these regions, HNF4A, but not FOXA2, is necessary for the active epigenetic state (Fig. 7).”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationown dataThe high level of H3K27ac and 5hmC at HBRs is likely due to HNF4A interactions with CBP/p300 and TET3 respectively.
“In summary, we show that HBRs are associated with a high level of H3K27ac and 5hmC, likely due to HNF4A interactions with CBP/p300 and TET3 respectively (Fig. 7).”
Quote in the paperSubstantial claim
The paper relies on this without support.
5hmC is produced by oxidation of 5mC due to activity of TET1, TET2 and TET3.
“DNA hydroxymethylation or 5-hydroxymethylcytosine (5hmC) is a recently discovered DNA modification that is produced by the oxidation of 5mC due to activity of ten-eleven translocation proteins (TET1, TET2 and TET3).”
The paper relies on this without support.
The mechanisms through which HNF4A exerts its functions are not well understood.
“However, the mechanisms through which HNF4A exerts its functions are not well understood.”
The paper relies on this without support.
The HNF4A antibody used for ChIP-seq identifies both embryonic and adult isoforms.
“HNF4A antibody (Table. S2) used for ChIP-seq identifies both embryonic and adult isoforms.”
The paper relies on this without support.
The role of HNF4A in epigenetic-mediated gene regulation in liver is not well defined.
“Although various TFs were shown to regulate gene expression by influencing histone (24, 37) and DNA modifications at gene regulatory regions (24, 37, 38), the role of HNF4A in epigenetic-mediated gene regulation in liver is not well defined.”
The paper relies on this without support.
Mouse HPPL cells are capable of generating hepatocyte and cholangiocytes similar to mouse hepatoblasts.
“Knockdown of HNF4A in mouse HPPL cells (hepatic progenitor cells proliferating on laminin), which are capable of generating hepatocyte and cholangiocytes similar to mouse hepatoblasts, caused a reduction of Tet3 mRNA expression (p<0.0001) and protein levels (Fig. 6B), suggesting that HNF4A regulates Tet3 expression in hepatic cells.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
EP300 is a histone acetyltransferase that acetylates enhancer regions and activates transcription, which promotes hepatoblast differentiation.
“EP300, a histone acetyltransferase, is one such epigenetic modifier that acetylates enhancer regions and activates transcription leading to hepatoblast differentiation41,42,.”
From Multi-zonal liver organoids from human pluripotent stem cells (2025) · cites this paper as [41]
The Introduction identifies CBP/p300 as a histone acetylase, and the Discussion says its interaction with HNF4A may account for H3K27 acetylation at enhancers. The Results link increased enhancer acetylation with gene expression during hepatoblast-to-hepatocyte differentiation, but the paper attributes that regulation to HNF4A; it does not establish that EP300 itself drives the differentiation. (LLM, conf=0.86)
Experimental — accuracy not yet measuredHNF4A bound regions (HBRs) are flanked by nucleosomes marked with H3K4me1.
“HNF4A bound regions (HBRs) are flanked by nucleosomes marked with H3K4me148–50, leading us to question whether HNF4A contributes to the establishment and maintenance of H3K4me1 at HBRs.”
From HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements (2024) · cites this paper as [48]
HNF4A is required for active histone and DNA signatures at enhancers.
“While we previously showed that HNF4A is required for active histone and DNA signatures at enhancers48, its involvement in establishing the primed state that is laid down prior to activation was not examined.”
From HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements (2024) · cites this paper as [48]
95% of our ~12,000 HBRs matched regions identified as bound by HNF4A in Reizel et al. data.
“we compared the adult mouse liver HNF4A ChIP-seq data from Reizel et al.52 to our HNF4A ChIP-seq data48,49 and observed that 95% of our ~12,000 HBRs matched regions identified as bound by HNF4A in their data (Supplementary Fig. 1d).”
From HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements (2024) · cites this paper as [48]
HNF4A interacts with TET proteins to maintain hydroxymethylation, an active DNA modification at enhancers.
“Previously, we determined that HNF4A interacts with TET proteins to maintain hydroxymethylation, an active DNA modification at enhancers48.”
From HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements (2024) · cites this paper as [48]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Human fibroblasts described for studies of mouse fibroblasts
MinorThe introduction describes the cited studies (25, 26) as using human fibroblasts, but the titles of both cited references say they used mouse fibroblasts.
“Studies transducing a combination of TFs into human fibroblasts to produce highly functional hepatocytes support HNF4A’s involvement in chromatin remodelling. These studies revealed that HNF4A is crucial for generating induced hepatocyte-like cells (iHeps) (25, 26)”
“25. Huang P, He Z, Ji S, Sun H, Xiang D, Liu C, Induction of functional hepatocyte-like cells from mouse fibroblasts by defined factors.”
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“5hmC plays an important role during mammalian development and cellular differentiation: Tet1/2/3 deficiency in embryonic stem cells (ESCs; triple-knockout cells) reduces their differentiation capabilities and also limits their developmental potential during embryogenesis.”
BackgroundInfluentialMutations in the hepatocyte nuclear factor-1α gene in maturity-onset diabetes of the young (MODY3)
Yamagata, K., Oda, N., Kaisaki, P. J., Menzel, S., Furuta, H., Vaxillaire, M., Southam, L., Cox, R., Lathrop, M. G., Boriraj, V. V., et al. (1996) · Nature · doi:10.1038/384455a0 · Cited by 1,610 · see citing works
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“It is well established that active enhancers are associated with high-5hmC and low-5mC DNA modifications.(14,33) To examine the level of 5mC and 5hmC at HBRs, we isolated hepatocytes from mouse liver and performed MeDIP and hMeDIP, followed by high-throughput sequencing.”
BackgroundMethodImpact of cytosine methylation on DNA binding specificities of human transcription factors
Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P. K., Kivioja, T., Dave, K., Zhong, F., et al. (2017) · Science · doi:10.1126/science.aaj2239 · Cited by 1,257 · cited 5× · see citing works
“Thus, H3K27ac at HNF4A binding sites could be affected by interactions with other TFs. Alternatively, HNF4A, with or without other factors, could have a protective effect that disallows histone deacetylases to act.”
BackgroundInfluentialHayhurst, G. P., Lee, Y.-H., Lambert, G., Ward, J. M., & Gonzalez, F. J. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.4.1393-1403.2001 · Cited by 1,107 · cited 3× · see citing works
“HNF4A is a key TF in liver given that its loss is associated with transcriptional repression of genes.(5,10) Although various TFs were shown to regulate gene expression by influencing histone(24,37) and DNA modifications at gene-regulatory regions,(24,37,38) the role of HNF4A in epigenetic-mediated gene regulation in…”
BackgroundSelf-citationSladek, F. M., Zhong, W. M., Lai, E., & Darnell, J. E. (1990) · Genes & Development · doi:10.1101/gad.4.12b.2353 · Cited by 1,027 · cited 1× · see citing works
“Hepatocyte nuclear factor 4A (HNF4A; also known as NR2A1) is a member of the nuclear receptor superfamily of transcription factors (TFs) and is expressed in the liver, pancreas, gastrointestinal tract, and kidneys.(1) In liver, HNF4A is required for normal development,(2) including morphogenesis(3) and differentiation…”
BackgroundMutations in the hepatocyte nuclear factor-4α gene in maturity-onset diabetes of the young (MODY1)
Yamagata, K., Furuta, H., Oda, N., Kaisaki, P. J., Menzel, S., Cox, N. J., Fajans, S. S., Signorini, S. G., Stoffel, M., & Bell, G. I. (1996) · Nature · doi:10.1038/384458a0 · Cited by 975 · cited 1× · see citing works
“(5) In humans, HNF4A mutations have been linked to maturity-onset diabetes of young type 1, a monogenic form of type 2 diabetes.(6) In addition to maintaining expression of various genes associated with metabolic processes in liver, several studies have connected reduced HNF4A expression with liver cancer progression.”
BackgroundInduction of functional hepatocyte-like cells from mouse fibroblasts by defined factors
Huang, P., He, Z., Ji, S., Sun, H., Xiang, D., Liu, C., Hu, Y., Wang, X., & Hui, L. (2011) · Nature · doi:10.1038/nature10116 · Cited by 864 · cited 1× · see citing works
“These studies revealed that HNF4A is crucial for generating induced hepatocyte-like cells (iHeps),(25,26) given that HNF4A overexpression alone may be sufficient to generate these cells.”
BackgroundDirect conversion of mouse fibroblasts to hepatocyte-like cells by defined factors
Sekiya, S., & Suzuki, A. (2011) · Nature · doi:10.1038/nature10263 · Cited by 846 · cited 1× · see citing works
“These studies revealed that HNF4A is crucial for generating induced hepatocyte-like cells (iHeps),(25,26) given that HNF4A overexpression alone may be sufficient to generate these cells.”
BackgroundGenome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
Pastor, W. A., Pape, U. J., Huang, Y., Henderson, H. R., Lister, R., Ko, M., McLoughlin, E. M., Brudno, Y., Mahapatra, S., Kapranov, P., et al. (2011) · Nature · doi:10.1038/nature10102 · Cited by 804 · see citing works
Transcription factors as readers and effectors of DNA methylation
Zhu, H., Wang, G., & Qian, J. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.83 · Cited by 649 · cited 1× · see citing works
“Histone modifications have been associated with repressed, poised, and active enhancers and promoters and, ultimately, control gene activity.(13,14) In particular, lysine 4 of histone 3 monomethylation (H3K4me1) and trimethylation (H3K4me3) mark enhancers and promoters, respectively.”
BackgroundMammalian hepatocyte differentiation requires the transcription factor HNF-4alpha.
(2000) · PubMed Central · Cited by 489 · see citing works
Boyes, J., & Bird, A. (1992) · The EMBO Journal · doi:10.1002/j.1460-2075.1992.tb05055.x · Cited by 471 · cited 1× · see citing works
“DNA methylation (5-methylcytosine; 5mC) is associated with gene repression(16) and can disrupt the binding of many TFs.”
BackgroundMammalian hepatocyte differentiation requires the transcription factor HNF-4αPreprint
Li, J., Ning, G., & Duncan, S. A. (2000) · Genes & Development · doi:10.1101/gad.14.4.464 · Cited by 458 · cited 5× · see citing works
“HNF4A deficiency in mouse embryonic liver causes failure in hepatocyte differentiation,(2) whereas in adult mice loss of HNF4A affects lipid homeostasis leading to liver steatosis.”
BackgroundInfluentialIwafuchi-Doi, M., Donahue, G., Kakumanu, A., Watts, J. A., Mahony, S., Pugh, B. F., Lee, D., Kaestner, K. H., & Zaret, K. S. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.03.001 · Cited by 390 · cited 1× · see citing works
“(11) As a pioneer factor, FOXA family members are capable of altering epigenetic modifications to regulate gene expression.(24,34) We therefore speculated that a high level of H3K4me1 and H3K27ac at HBRs could be attributed to FOXA2 occupancy at those sites.”
BackgroundKreamer, B. L., Staecker, J. L., Sawada, N., Sattler, G. L., Hsia, M. T. S., & Pitot, H. C. (1986) · In Vitro Cellular & Developmental Biology - Plant · doi:10.1007/bf02623304 · Cited by 383 · cited 1× · see citing works
“Hepatocytes were separated by low-speed centrifugation (50g × 30 seconds).(28) Hepatoblast isolation from E14.”
MethodLoss of Tet Enzymes Compromises Proper Differentiation of Embryonic Stem Cells
Dawlaty, M. M., Breiling, A., Le, T., Barrasa, M. I., Raddatz, G., Gao, Q., Powell, B. E., Cheng, A. W., Faull, K. F., Lyko, F., et al. (2014) · Developmental Cell · doi:10.1016/j.devcel.2014.03.003 · Cited by 338 · see citing works
Hnf4: A Central Regulator of Hepatocyte Differentiation and Function
Watt, A. J., Garrison, W. D., & Duncan, S. A. (2003) · Hepatology · doi:10.1053/jhep.2003.50273 · Cited by 307 · cited 2× · see citing works
“HNF4A is a key TF in liver given that its loss is associated with transcriptional repression of genes.(5,10) Although various TFs were shown to regulate gene expression by influencing histone(24,37) and DNA modifications at gene-regulatory regions,(24,37,38) the role of HNF4A in epigenetic-mediated gene regulation in…”
BackgroundMethylome analysis using MeDIP-seq with low DNA concentrations
Taiwo, O., Wilson, G. A., Morris, T. J., Seisenberger, S., Reik, W., Pearce, D., Beck, S., & Butcher, L. M. (2012) · Nature Protocols · doi:10.1038/nprot.2012.012 · Cited by 294 · cited 1× · see citing works
“Low-input MeDIP sequencing and hMeDIP sequencing were as described.(29) DNA was sonicated to 200-400 base pairs (bp) using E-220 sonicator (Covaris), followed by end repair adapter ligation, and immunoprecipitation using anti-5mC or anti-5hmC antibodies.”
MethodHepatocyte Nuclear Factor 4α Suppresses the Development of Hepatocellular Carcinoma
Ning, B., Ding, J., Yin, C., Zhong, W. H., Wu, K., Zeng, X. Y., Yang, W. K., Chen, Y.-X., Zhang, J., Zhang, X., et al. (2010) · Cancer Research · doi:10.1158/0008-5472.can-10-0824 · Cited by 241 · see citing works
Hong, Y. H., Varanasi, U. S., Yang, W., & Leff, T. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m304112200 · Cited by 220 · cited 1× · see citing works
“HEK293T cells were transfected with an HNF4A expression vector(32) and hemagglutinin-tagged TET3 vector (Addgene #49446) alone and in combination using polyethylenimine.”
MethodHNF4A is essential for specification of hepatic progenitors from human pluripotent stem cells
DeLaForest, A., Nagaoka, M., Si-Tayeb, K., Noto, F. K., Konopka, G., Battle, M. A., & Duncan, S. A. (2011) · Development · doi:10.1242/dev.062547 · Cited by 219 · cited 1× · see citing works
“(1) In liver, HNF4A is required for normal development,(2) including morphogenesis(3) and differentiation,(4) and controls other TFs critical in liver cell fate as well as genes necessary for hepatocyte functions.”
BackgroundDUX4 recruits p300/CBP through its C-terminus and induces global H3K27 acetylation changes
Choi, S. H., Gearhart, M. D., Cui, Z., Bosnakovski, D., Kim, M., Schennum, N., & Kyba, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw141 · Cited by 196 · cited 1× · see citing works
“1362 may be controlled by TFs directly or indirectly interacting with epigenetic modifiers,(21) such as the histone acetylase, cAMP-response element-binding protein (CREB)-binding protein (CBP)/p300.(22) Recent reports have identified TFs that interact with TET proteins to maintain low 5mC and high 5hmC at enhancers.”
BackgroundSuppression of Hepatocyte Proliferation by Hepatocyte Nuclear Factor 4α in Adult Mice
Bonzo, J. A., Ferry, C. H., Matsubara, T., Kim, J.-H., & Gonzalez, F. J. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.334599 · Cited by 193 · cited 4× · see citing works
“(11) AlbERT2creand Hnf4aFl/Fl mouse lines were described in an earlier study.(4) These two mouse strains were crossed to produce tamoxifen-inducible, hepatocyte-specific cre-recombinase–expressing mouse.”
BackgroundMethodInfluentialSelf-citationRobertson, A. G., Bilenky, M., Tam, A., Zhao, Y., Zeng, T., Thiessen, N., Cezard, T., Fejes, A. P., Wederell, E. D., Cullum, R., et al. (2008) · Genome Research · doi:10.1101/gr.078519.108 · Cited by 182 · cited 6× · see citing works
“ChIP sequencing (ChIPseq) library construction and Illumina Genome Analyzer sequencing was performed as described.(15) Bioinformatic analysis of ChIP-seq data was performed as described in the Supporting Materials and Methods section.”
BackgroundMethodInfluentialSelf-citationSchübeler, D., Lorincz, M. C., Cimbora, D. M., Telling, A., Feng, Y.-Q., Bouhassira, E. E., & Groudine, M. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.24.9103-9112.2000 · Cited by 165 · see citing works
Wederell, E. D., Bilenky, M., Cullum, R., Thiessen, N., Dagpinar, M., Delaney, A., Varhol, R., Zhao, Y., Zeng, T., Bernier, B., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn382 · Cited by 150 · cited 1× · see citing works
“Chromatin immunoprecipitation (ChIP) was performed as described,(30) with the following modifications.”
MethodSelf-citationSRC-1 and GRIP1 Coactivate Transcription with Hepatocyte Nuclear Factor 4
Wang, J.-C., Stafford, J. M., & Granner, D. K. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.47.30847 · Cited by 147 · cited 1× · see citing works
“In addition to FOXA family members, HNF4A was previously shown to recruit several coactivators, such as glucocorticoid receptor interacting protein 1, steroid receptor coactivator 1, and CREBs, to regulate gene expression.(41,43) The role of these co-factors is not clear.”
BackgroundTET3 Is Recruited by REST for Context-Specific Hydroxymethylation and Induction of Gene Expression
Perera, A., Eisen, D., Wagner, M., Laube, S. K., Künzel, A. F., Koch, S., Steinbacher, J., Schulze, E., Splith, V., Mittermeier, N., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.03.020 · Cited by 145 · see citing works
Jin, S.-G., Zhang, Z.-M., Dunwell, T. L., Harter, M. R., Wu, X., Johnson, J., Li, Z., Liu, J., Szabó, P. E., Lu, Q., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2015.12.044 · Cited by 138 · cited 1× · see citing works
“A recent study showed that TET3 can identify and facilitate removal of 5caC by base excision repair to achieve demethylation of gene-regulatory regions.(47) Thus, future work is needed to examine the entire 5mC oxidation pathway in liver.”
BackgroundPPARγ-induced PARylation promotes local DNA demethylation by production of 5-hydroxymethylcytosine
Fujiki, K., Shinoda, A., Kano, F., Sato, R., Shirahige, K., & Murata, M. (2013) · Nature Communications · doi:10.1038/ncomms3262 · Cited by 123 · cited 1× · see citing works
“(22) Recent reports have identified TFs that interact with TET proteins to maintain low 5mC and high 5hmC at enhancers.(23,24) Studies transducing a combination of TFs into human fibroblasts to produce highly functional hepatocytes support HNF4A’s involvement in chromatin remodelling.”
BackgroundSantangelo, L., Marchetti, A., Cicchini, C., Conigliaro, A., Conti, B., Mancone, C., Bonzo, J. A., Gonzalez, F. J., Alonzi, T., Amicone, L., et al. (2011) · Hepatology · doi:10.1002/hep.24280 · Cited by 121 · cited 1× · see citing works
“1361 epithelial-to-mesenchymal transition (EMT), a process associated with cancer progression.(8) Conversely, its overexpression in hepatocellular carcinoma rodent models shows its role in tumor suppression(4,7) by repressing the proliferative capacity of cancer cells.”
BackgroundSelf-citationHippo Signaling Influences HNF4A and FOXA2 Enhancer Switching during Hepatocyte Differentiation
Alder, O., Cullum, R., Lee, S., Kan, A. C., Wei, W., Yi, Y., Garside, V. C., Bilenky, M., Griffith, M., Morrissy, A. S., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.08.046 · Cited by 113 · cited 21× · see citing works
“5 livers was as described.(11) AlbERT2creand Hnf4aFl/Fl mouse lines were described in an earlier study.”
BackgroundMethodInfluentialSelf-citationHolloway, M. G., Miles, G. D., Dombkowski, A. A., & Waxman, D. J. (2008) · Molecular Endocrinology · doi:10.1210/me.2007-0564 · Cited by 108 · cited 1× · see citing works
“(39) In addition, HNF4A may regulate chromatin indirectly by controlling expression of chromatin remodeling genes, such as SWI/ SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 and chromatin licensing and DNA replication factor 1, given that their expression is altered in HNF4A…”
BackgroundFunctional Association between CBP and HNF4 inTrans-activation
Yoshida, E., Aratani, S., Itou, H., Miyagishi, M., Takiguchi, M., Osumu, T., Murakami, K., & Fukamizu, A. (1997) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.1997.7871 · Cited by 104 · see citing works
Mueller, B., Mieczkowski, J., Kundu, S., Wang, P., Sadreyev, R., Tolstorukov, M. Y., & Kingston, R. E. (2017) · Genes & Development · doi:10.1101/gad.293118.116 · Cited by 100 · cited 1× · see citing works
“(11) Genome-wide epigenetic analysis has proven that active cis-regulatory regions are located in open chromatin regions,(12) whereas condensed chromatin is inaccessible and thus inactive.”
BackgroundWalesky, C. M., Gunewardena, S., Terwilliger, E. F., Edwards, G., Borude, P. C., & Apte, U. M. (2012) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00064.2012 · Cited by 93 · cited 1× · see citing works
“(8) Conversely, its overexpression in hepatocellular carcinoma rodent models shows its role in tumor suppression(4,7) by repressing the proliferative capacity of cancer cells.(9) Taken together, these studies strongly support a role for HNF4A as a central regulator of hepatocyte identity by playing a crucial function…”
BackgroundLong-term culture of hepatic progenitors derived from mouse Dlk+ hepatoblasts
Tanimizu, N., Saito, H., Mostov, K. E., & Miyajima, A. (2004) · Journal of Cell Science · doi:10.1242/jcs.01572 · Cited by 87 · see citing works
Postnatal DNA demethylation and its role in tissue maturation
Reizel, Y., Sabag, O., Skversky, Y., Spiro, A., Steinberg, B., Bernstein, D., Wang, A., Kieckhaefer, J., Li, C., Pikarsky, E., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04456-6 · Cited by 83 · see citing works
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Yang, Y. A., Zhao, J. C., Fong, K.-W., Kim, J., Li, S., Song, C., Song, B., Zheng, B., He, C., & Yu, J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw498 · Cited by 69 · see citing works
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ChAsE: chromatin analysis and exploration tool
Younesy, H., Nielsen, C. B., Lorincz, M. C., Jones, S. J. M., Karimi, M. M., & Möller, T. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw382 · Cited by 41 · cited 3× · see citing works
“To address this, we performed K-means clustering (K = 5) on HBRs and FBRs in hepatocytes using ChAsE(35) and identified five clusters.”
MethodInfluentialSelf-citationAncey, P., Ecsedi, S., Lambert, M.-P., Talukdar, F. R., Cros, M., Glaise, D., Narváez, D. M., Chauvet, V., Herceg, Z., Corlu, A., et al. (2017) · Stem Cell Reports · doi:10.1016/j.stemcr.2017.05.023 · Cited by 41 · see citing works
Guan, W., Guyot, R., Samarut, J., Flamant, F., Wong, J., & Gauthier, K. C. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1702192114 · Cited by 32 · cited 5× · see citing works
“Thus, H3K27ac at HNF4A binding sites could be affected by interactions with other TFs. Alternatively, HNF4A, with or without other factors, could have a protective effect that disallows histone deacetylases to act.”
BackgroundInfluentialSelf-citationZhang, Q., Lei, X., & Lu, H. (2014) · PLoS ONE · doi:10.1371/journal.pone.0084925 · Cited by 16 · see citing works
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- 2015, TET3 is recruited by REST for context‐specific hydroxymethylation and induction of gene expression, Cell Rep, 11, 283, 10.1016/j.celrep.2015.03.020 · DOI · Paper page
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Sorted by citations
TET (Ten-eleven translocation) family proteins: structure, biological functions and applications
Zhang, X., Zhang, Y., Wang, C., & Wang, X. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01537-x · Cited by 286 · see citing works
Chromatin accessibility: biological functions, molecular mechanisms and therapeutic application
Chen, Y., Liang, R., Li, Y., Jiang, L., Ma, D., Luo, Q., & Song, G. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-02030-9 · Cited by 174 · see citing works
“158 HNF4 α enriched H3K4me1 and H3K27ac modi fi cation to maintain opening chromatin at active transcriptional regions.”
Bipotent transitional liver progenitor cells contribute to liver regeneration
Pu, W., Zhu, H., Zhang, M., Pikiolek, M., Ercan, C., Li, J., Huang, X., Han, X., Zhang, Z., Lv, Z., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01335-9 · Cited by 138 · see citing works
The Role of CYP3A in Health and Disease
Klyushova, L. S., Perepechaeva, M. L., & Grishanova, A. Y. (2022) · Biomedicines · doi:10.3390/biomedicines10112686 · Cited by 105 · see citing works
“Moreover, HNF4α regulates TET3 expression in the liver by direct binding to an enhancer region [62].”
BackgroundLoss of liver function in chronic liver disease: An identity crisis
Berasain, C., Arechederra, M., Argemí, J., Fernández-Barrena, M. G., & Avila, M. A. (2023) · Journal of Hepatology · doi:10.1016/j.jhep.2022.09.001 · Cited by 99 · see citing works
Multi-zonal liver organoids from human pluripotent stem cells
Reza, H. A., Santangelo, C., Iwasawa, K., Reza, A. A., Sekiya, S., Glaser, K., Bondoc, A., Merola, J., & Takebe, T. (2025) · Nature · doi:10.1038/s41586-025-08850-1 · Cited by 71 · see citing works
Zhang, T., Wang, T., Niu, Q., Xu, L., Chen, Y., Gao, H., Gao, H., Zhang, L., Li, J., Li, J., et al. (2022) · BMC Biology · doi:10.1186/s12915-022-01269-4 · Cited by 67 · see citing works
“HNF4A as a member of the transcriptional regulators of the HNF4 family enriched in the liver was critical for bile acid homeostasis and bile duct development [94].”
BackgroundQu, M., Qu, H., Jia, Z., & Kay, S. A. (2021) · Nature Communications · doi:10.1038/s41467-021-26567-3 · Cited by 65 · see citing works
Control of Cell Identity by the Nuclear Receptor HNF4 in Organ Pathophysiology
Dubois, V., Staels, B., Lefebvre, P., Verzi, M., & Eeckhoute, J. (2020) · Cells · doi:10.3390/cells9102185 · Cited by 63 · see citing works
“In murine hepatocytes, HNF4A is essential for establishing and maintaining active histone and DNA epigenetic states at CRMs through interaction with E1A Binding Protein P300 (EP300) and Tet Methylcytosine Dioxygenase 3 (TET3), respectively [108].”
BackgroundCollapse of the hepatic gene regulatory network in the absence of FoxA factors
Reizel, Y., Morgan, A., Gao, L., Lan, Y., Manduchi, E., Waite, E. L., Wang, A. W., Wells, A., & Kaestner, K. H. (2020) · Genes & Development · doi:10.1101/gad.337691.120 · Cited by 60 · see citing works
“Third, recently Thakur and colleagues analyzed the epigenetic role of HNF4α and FoxA2 in adult liver and concluded that FoxA2 has no significant role in maintaining enhancer activity in the adult liver (Thakur et al. 2019).”
BackgroundFetal liver development and implications for liver disease pathogenesis
Lotto, J., Stephan, T. L., & Hoodless, P. A. (2023) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-023-00775-2 · Cited by 47 · see citing works
Self-citationProtein Interactions at Oxidized 5-Methylcytosine Bases
Pfeifer, G. P., Szabó, P. E., & Song, J. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.07.039 · Cited by 49 · see citing works
Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver
Dubois, V., Gheeraert, C., Vankrunkelsven, W., Dubois‐Chevalier, J., Dehondt, H., Bobowski‐Gerard, M., Vinod, M., Zummo, F. P., Güiza, F., Ploton, M., et al. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199156 · Cited by 46 · see citing works
“Considering that LIVER-ID TFs target EP300 at liver CRMs to catalyze H3K27ac (Thakur et al, 2019), through their interaction with EP300 (Appendix Fig S10A; Eeckhoute et al, 2004; Kemper et al, 2009; von Meyenn et al, 2013), we hypothesized that the ERS-mediated decrease in LIVER-ID TFs and H3K27ac…”
BackgroundLi, S., Zhu, Y., Li, R., Huang, J., You, K., Yuan, Y., & Zhuang, S. (2021) · Advanced Science · doi:10.1002/advs.202003094 · Cited by 44 · see citing works
Transcription Control of Liver Development
Tachmatzidi, E. C., Galanopoulou, O., & Talianidis, I. (2021) · Cells · doi:10.3390/cells10082026 · Cited by 45 · see citing works
Downregulation of HNF4A enables transcriptomic reprogramming during the hepatic acute-phase response
Ehle, C., Iyer-Bierhoff, A., Wu, Y., Xing, S., Kiehntopf, M., Mosig, A. S., Godmann, M., & Heinzel, T. (2024) · Communications Biology · doi:10.1038/s42003-024-06288-1 · Cited by 30 · see citing works
“HNF4AP1bindsto enhancers and promoters of > 50% of liver-speci fi c genes 6 , recruiting co-activators (e.g. P300, TET3) to establish active chromatin states associated with epigenetic modi fi cations such as histone H3K4me1, H3K27ac and 5-hydroxymethylation of cytosines 1,3,11 .”
BackgroundRamaker, R. C., Hardigan, A. A., Goh, S.-T., Partridge, E. C., Wold, B. J., Cooper, S. J., & Myers, R. (2020) · Genome Research · doi:10.1101/gr.260463.119 · Cited by 30 · see citing works
Lv, L., Zhao, Y., Wei, Q., Zhao, Y., & Yi, Q. (2020) · Cancer Cell International · doi:10.1186/s12935-020-01298-5 · Cited by 28 · see citing works
“It has been recently reported that HNF4A, a liver-enriched transcription factor, could upregulate gene expression in hepatocytes by binding the enhancers of target genes [24].”
BackgroundSengupta, I., Mondal, P., Sengupta, A., Mondal, A., Singh, V., Adhikari, S., Dhang, S., Roy, S., & Das, C. (2022) · FEBS Journal · doi:10.1111/febs.16544 · Cited by 23 · see citing works
Decoding YAP dependent transcription in the liver
Biagioni, F., Croci, O., Sberna, S., Donato, E., Sabò, A., Bisso, A., Curti, L., Chiesa, A., & Campaner, S. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac624 · Cited by 22 · see citing works
TET2 and TET3 loss disrupts small intestine differentiation and homeostasis
Ansari, I., Solé‐Boldo, L., Ridnik, M., Gutekunst, J., Gilliam, O., Korshko, M., Liwinski, T., Jickeli, B., Weinberg-Corem, N., Shoshkes-Carmel, M., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39512-3 · Cited by 23 · see citing works
“To understand the role of TET2 and TET3 in the SI, we generated intestinal-speci fi c TET2/3 double knock-out (dko) mice by crossing Tet2/3 fl / fl (wt) with VillinCre mice.”
The protein architecture and allosteric landscape of HNF4α
Rastinejad, F. (2023) · Frontiers in Endocrinology · doi:10.3389/fendo.2023.1219092 · Cited by 26 · see citing works
Wnt/β-catenin signaling pathway in liver biology and tumorigenesis
Matsumoto, S., & Kikuchi, A. (2024) · In Vitro Cellular & Developmental Biology - Animal · doi:10.1007/s11626-024-00858-7 · Cited by 24 · see citing works
Signalling pathways and transcriptional regulators orchestrating liver development and cancer
Campbell, S. A., Stephan, T. L., Lotto, J., Cullum, R., Drissler, S., & Hoodless, P. A. (2021) · Development · doi:10.1242/dev.199814 · Cited by 22 · see citing works
Self-citationWang, C., Yu, H., Lu, S., et al. (2022) · Redox Biology · doi:10.1016/j.redox.2022.102498 · Cited by 22 · see citing works
The role of FOXA family transcription factors in glucolipid metabolism and NAFLD
Yu, C., Li, X., Zhao, Y., & Hu, Y. (2023) · Frontiers in Endocrinology · doi:10.3389/fendo.2023.1081500 · Cited by 22 · see citing works
“This is consistent with the previous report of significant overlap between HNF4a and FOXA2 binding regions in hepatocytes (33).”
ResultFoxA factors: the chromatin key and doorstop essential for liver development and functionPreprint
Heslop, J. A., & Duncan, S. A. (2020) · Genes & Development · doi:10.1101/gad.340570.120 · Cited by 19 · see citing works
“Thus, the expression of a significant cluster of hepatic genes is likely dependent on FoxA to induce and maintain chromatin accessibility and for HNF4α to recruit transcriptional complexes (Delaforest et al. 2019; Thakur et al. 2019).”
BackgroundMartínez‐Calle, M., Courbon, G., Hunt-Tobey, B., Francis, C., Spindler, J. J., Wang, X., dos Reis, L. M., Martins, C. S. W., Salusky, I. B., Malluche, H. H., et al. (2023) · Journal of Clinical Investigation · doi:10.1172/jci159928 · Cited by 17 · see citing works
“%) at gene promoters (17) (Figure 3D).”
Fan, Y., Qian, H., Zhang, M., Tao, C., Li, Z., Yan, W., Huang, Y., Zhang, Y., Xu, Q., Wang, X., et al. (2023) · Genome biology · doi:10.1186/s13059-023-02938-5 · Cited by 17 · see citing works
“HNF4α, as a nuclear receptor, can bind to the genome to maintain chromatin structure and regulate gene expression in hepatocytes [25].”
BackgroundAndrographolide modulates HNF4α activity imparting on hepatic metabolism
Zhang, M., Yang, M., Wang, N., Liu, Q., Wang, B., Huang, T., Tong, Y., Ming, Y., Wong, C., Liu, J., et al. (2020) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2020.110867 · Cited by 16 · see citing works
Disruption of Tumor Suppressors HNF4α/HNF1α Causes Tumorigenesis in Liver
Teeli, A. S., Łuczyńska, K., Haque, E., Gayas, M. A., Winiarczyk, D., & Taniguchi, H. (2021) · Cancers · doi:10.3390/cancers13215357 · Cited by 16 · see citing works
“Additionally, TET3 interacts with HNF4α and maintains both acetylation of lysine 27 of histone 3 (H3K27ac) and 5-hydroxymethylcytosine (5hmc) [105], which, in turn, controls the active epigenetic state of enhancers that induce transcription of genes in hepatocytes.”
BackgroundPeng, X., Li, H., Wang, D., Wu, L. Y., Hu, J., Ye, F., Syed, B. M., Liu, D., Zhang, J., & Liu, Q. (2023) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2023.133405 · Cited by 15 · see citing works
Matsumoto, S., Harada, A., Seta, M., Akita, M., Gon, H., Fukumoto, T., & Kikuchi, A. (2023) · Cancer Research · doi:10.1158/0008-5472.can-22-3518 · Cited by 15 · see citing works
Chen, Y., Zhang, T., Wu, L., et al. (2020) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.0c00047 · Cited by 14 · see citing works
Suzuki, T., Furuhata, E., Maeda, S., Kishima, M., Miyajima, Y., Tanaka, Y., Lim, J., Nishimura, H., Nakanishi, Y., Shojima, A., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03365-1 · Cited by 14 · see citing works
Lu, Y., Yu, Y., Liu, F., Han, Y., Xue, H.-G., Sun, X., Jiang, Y., & Tian, Z. (2020) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00243.2020 · Cited by 13 · see citing works
Liu, G., Wang, L., Wess, J., & Dean, A. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac707 · Cited by 12 · see citing works
Lickwar, C. R., Davison, J. M., Kelly, C., Mercado, G. P., Wen, J., Davis, B. R., Tillman, M., Semova, I., Andres, S. F., Vale, G., et al. (2021) · bioRxiv · doi:10.1016/j.jcmgh.2022.04.013 · Cited by 11 · see citing works
“what contributes to altered H3K27ac levels in our experiment, though TF candidates like HNF4A may recruit HDACs and histone acetyltransferases (Armour et al. 2017; Thakur et al. 2019).”
BackgroundPolymorphisms rs55710213 and rs56334587 regulate SCD1 expression by modulating HNF4A binding
Pan, G., Cavalli, M., & Wadelius, C. (2021) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2021.194724 · Cited by 11 · see citing works
“The enrichment of HNF4A binding to regulatory regions can be either caused by HNF4A direct binding or indirectly through protein partners in complex with HNF4A [37].”
BackgroundHNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements
Thakur, A., Park, K., Cullum, R., Fuglerud, B. M., Khoshnoodi, M., Drissler, S., Stephan, T. L., Lotto, J., Kim, D., Gonzalez, F. J., et al. (2024) · Communications Biology · doi:10.1038/s42003-024-05835-0 · Cited by 10 · see citing works
“While a concurrence of HNF4A binding and H3K4me1 has been well documented 48 – 50, 52, 60 , we show that HNF4A is essential essential for maintaining H3K4me1 at HBRs, and consequently H3K27ac , in the adult mouse Previously, we determined that HNF4A interacts with TET proteins to maintain…”
BackgroundMethodInfluentialSelf-citationHIF1α/miR-146α/TRAF6/NF-κB axis modulates hepatic iron overload-induced inflammation
Mo, F., Tang, Y., Shen, H., Wu, L., Liu, Q., Nie, S., Li, M., & Ling, C. (2023) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2023.109499 · Cited by 9 · see citing works
Signaling molecules orchestrating liver regenerative medicine
Zakeri, N., Mirdamadi, E. S., Kalhori, D., & Solati‐Hashjin, M. (2020) · Journal of Tissue Engineering and Regenerative Medicine · doi:10.1002/term.3135 · Cited by 9 · see citing works
“It has been postulated that by HNF-4-mediated remodeling of the transcriptionally inactive densified chromatin structures, regulating domains of genes (promoters and enhancers) are presumably opened up and consequently induce the gene expression (Thakur et al., 2019; Yin et al., 2011).”
BackgroundFXR Friend-ChIPs in the Enterohepatic System
Meadows, V., Yang, Z., Basaly, V., & Guo, G. L. (2023) · Seminars in Liver Disease · doi:10.1055/a-2128-5538 · Cited by 8 · see citing works
Qin, Z., Li, Y., Shao, X., Li, K., Bai, Y., Wang, B., Ma, F., Shi, W., Song, L., Zhuang, A., et al. (2025) · Cancer Letters · doi:10.1016/j.canlet.2025.217732 · Cited by 6 · see citing works
Hepatocyte nuclear factor 4-Alpha: a key regulator in liver carcinogenesis
Hamdy, H., Shen, C., Xu, J., Fan, D., Zhang, Y., Li, H., Wei, Y., & Sun, J. (2025) · Cellular Oncology · doi:10.1007/s13402-025-01064-7 · Cited by 6 · see citing works
“HNF4α’s pivotal role in hepatocyte development and func - tion suggests an indirect influence on phagocytosis, poten - tially through regulation of genes governing Kupffer cells differentiation, activation, and phagocytic capacity [ 68, 69].”
Singha, D., Mondal, M., Ghosh, D., Choudhury, D., Chakravarti, B., Kar, R. K., & Malakar, P. (2024) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1831 · Cited by 6 · see citing works
Liver gene regulatory networks: Contributing factors to nonalcoholic fatty liver disease
Cebola, I. (2020) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1480 · Cited by 5 · see citing works
Evidence of widespread, independent sequence signature for transcription factor cobindingPreprint
Zhou, M., Li, H., Wang, X., & Guan, Y. (2020) · Genome Research · doi:10.1101/gr.267310.120 · Cited by 6 · see citing works
Ascensión, A. M., & Araúzo-Bravo, M. J. (2020) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2020.3043979 · Cited by 4 · see citing works
“HNF4A: Regulates the expression of several hepatic genes and may play a role in the development of the liver, kidney, and intestines [End] [52].”
BackgroundSelf-Assembled Generation of Multi-zonal Liver Organoids from Human Pluripotent Stem CellsPreprint
Reza, H. A., Santangelo, C., Reza, A. A., Iwasawa, K., Sachiko, S., Glaser, K., Bondoc, A. J., Merola, J., & Takebe, T. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.30.610426 · Cited by 4 · see citing works
Zhang, F., Yao, Z., Gao, H., Shi, R., Xu, Y., Zhang, C., Zhao, P., Li, T., Cheng, Z., Zha, Y., et al. (2025) · Hepatology International · doi:10.1007/s12072-025-10916-1 · Cited by 3 · see citing works
“Additionally, several studies have reported that the liver-specific transcription factor HNF4A can directly interact with P300, and it often binds to certain regions together with FOXA2 to maintain H3K27ac enrichment at these sites [41, 42].”
HNF4α as a Master Regulator of Epigenetic Dynamics in Epithelial Cells
Amicone, L., Cicchini, C., & Marchetti, A. (2025) · Genes · doi:10.3390/genes17010041 · Cited by 3 · see citing works
Hernández-Banqué, C., Jové-Juncà, T., Crespo‐Piazuelo, D., González-Rodríguez, O., Ramayo‐Caldas, Y., Esteve‐Codina, A., Mercat, M.-J., Bink, M. C. A. M., Quintanilla, R., & Ballester, M. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1250942 · Cited by 3 · see citing works
“Hepatocyte nuclear factor 4 alpha (HNF4a) encodes for a protein that controls the expression of several hepatic genes, HNF1a among them, and plays a role in liver development (62, 63).”
Xu, C., Fang, X., Song, Y., Xiang, Z., Xu, X., & Wei, X. (2024) · International Journal of Biological Sciences · doi:10.7150/ijbs.93739 · Cited by 2 · see citing works
“Genome-wide promoter studies in adult liver have shown that HNF4α binds more than 40% of active gene promoters [91] and occupies active enhancers in hepatocytes to increase transcription of intracellular genes [ 92].”
BackgroundEpigenetic regulation in MASLD – insight for therapeutic target discovery
Britsemmer, J. H., López‐Alcántara, N., & Kirchner, H. (2026) · Epigenomics · doi:10.1080/17501911.2026.2633978 · Cited by 2 · see citing works
“HNF4α binding in enhancer regions during hepatocyte differentiation is necessary to maintain active H3K27ac marks and governs Tet3 expression in HPPL cells [88].”
Establishment of a Fah-LSL mouse model to study BEC-to-hepatocyte conversion
Wang, X., Pu, W., Zhu, H., Zhang, M., & Zhou, B. (2023) · Biophysics Reports · doi:10.52601/bpr.2023.230034 · Cited by 2 · see citing works
“…mice, whose tdT could be only expressed after the TAM-induced removal of two Stop sequences by both Dre-rox (HNF4α+) (Han et al. 2019; Thakur et al. 2019) and Cre-loxP (CK19+) recombinations; we also characterized BEC-derived transitional liver progenitor cells (TLPCs) by…”
BackgroundPparα and fatty acid oxidation coordinate hepatic transcriptional architecturePreprint
Cavagnini, K. S., & Wolfgang, M. J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.12.451949 · Cited by 2 · see citing works
AMPK activation prevents hepatocellular carcinoma development through inhibition of HNF4α activityPreprint
Sun, Z., Linares, B., Urdiales, C., Al-sarmi, F., Putluri, N., & Nostrand, J. L. V. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.16.652569 · Cited by 2 · see citing works
TBX3 advances the developmental chromatin landscape toward the hepatic fate
Stephan, T. L., Cullum, R., Drissler, S., Thomas, A., Fuglerud, B. M., Clement-Ranney, M., Lotto, J., Krentz, N. A. J., Duncan, S. A., & Hoodless, P. A. (2025) · Developmental Cell · doi:10.1016/j.devcel.2025.05.014 · Cited by 1 · see citing works
Self-citationAssociation between HNF4A rs1800961 polymorphisms and gallstones in a Taiwanese population
Lin, Y., Chen, I., Chen, Y., et al. (2023) · Journal of Gastroenterology and Hepatology · doi:10.1111/jgh.16426 · Cited by 1 · see citing works
“21 In the liver, HNF4A regulates the expression of several cholesterol transporters involved in bile metabolism.”
BackgroundSuzuki, T., Furuhata, E., Maeda, S., Kishima, M., Miyajima, Y., Tanaka, Y., Lim, J., Nishimura, H., Nakanish, Y., Shojima, A., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.16.423165 · Cited by 1 · see citing works
Fan, Y., Qian, H., Zhang, M., Tao, C., Li, Z., Yan, W., Huang, Y., Zhang, Y., Xu, Q., Wang, X., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22724288
Fan, Y., Qian, H., Zhang, M., Tao, C., Li, Z., Yan, W., Huang, Y., Zhang, Y., Xu, Q., Wang, X., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22724276
Fan, Y., Qian, H., Zhang, M., Tao, C., Li, Z., Yan, W., Huang, Y., Zhang, Y., Xu, Q., Wang, X., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22724273
Fan, Y., Qian, H., Zhang, M., Tao, C., Li, Z., Yan, W., Huang, Y., Zhang, Y., Xu, Q., Wang, X., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22724291
Fan, Y., Qian, H., Zhang, M., Tao, C., Li, Z., Yan, W., Huang, Y., Zhang, Y., Xu, Q., Wang, X., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22724282
Fan, Y., Qian, H., Zhang, M., Tao, C., Li, Z., Yan, W., Huang, Y., Zhang, Y., Xu, Q., Wang, X., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22724279
Telles-Silva, K. A., Pacheco, L. V. B., Komatsu, S., Chianca, F., Chagas, G., Martins, G. C., Gridina, M. M., Panchenko, D., Carvalho, V. M., Caldini, E. T. E. G., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.17.660221
Fan, Y., Qian, H., Zhang, M., Tao, C., Li, Z., Yan, W., Huang, Y., Zhang, Y., Xu, Q., Wang, X., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22724294
Fan, Y., Qian, H., Zhang, M., Tao, C., Li, Z., Yan, W., Huang, Y., Zhang, Y., Xu, Q., Wang, X., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22724270
Mononen, J., Taipale, M., Malinen, M., Levonen, A., Ruotsalainen, A., Norton, L., & Heikkinen, S. (2026) · PLoS Genetics · doi:10.1371/journal.pgen.1011716
“…several studies have shown that TFs can have cell-type-specific properties related to chromatin accessibility moderation, i.e., pioneer-like activity, which highlights the need for addressing the complex relationship of TF binding, genetics and chromatin accessibility in more depth [13–18].”
Sun, Z., Linarés, B., Urdiales, C., Al-sarmi, F., Sang, B., Putluri, N., & Nostrand, J. L. V. (2026) · Science Advances · doi:10.1126/sciadv.aea8017
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FOXM1 inhibition primes terminal differentiation of human iPSC-derived hepatocytes
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- Authors
- Thakur, A., Wong, J. C. H., Wang, E. Y., Lotto, J., Kim, D., Cheng, J., Mingay, M., Cullum, R., Moudgil, V., Ahmed, N., Tsai, S., Wei, W., Walsh, C. P., Stephan, T., Bilenky, M., Fuglerud, B. M., Karimi, M. M., Gonzalez, F. J., Hirst, M., & Hoodless, P. A.
- Affiliations
- BC Cancer Agency (CA)
- University of British Columbia (CA)
- National Cancer Institute (US)
- University of Ulster (GB)
- MRC London Institute of Medical Sciences (GB)
- Corresponding author
- Hoodless, Pamela A.
- ORCID
- Venue
- Hepatology
- Published
- 2019-05-15
- Volume
- 70
- Issue
- 4
- Pages
- 1360-1376
- ISSN
- 0270-9139 (ISSN-L)
- 1527-3350
- PMC
- PMC6773525
- OpenAlex
- W2934729452
- Cited by
- 75
- References
- 48
- Citations by year
- 2026: 7 · 2025: 8 · 2024: 7 · 2023: 17 · 2022: 9 · 2021: 7 · 2020: 15 · 2019: 2
- FWCI
- 2.60
- Type
- journal article
- Language
- en
- Open access
- green
- pure.ulster.ac.uk
- Licence
- Locations
- Hepatology (publishedVersion)
- PubMed (publishedVersion)
- Ulster University Research Portal (Ulster University) (publishedVersion, other-oa)
- PubMed Central (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Health Sciences › Medicine › Surgery › Pancreatic function and diabetes
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Cancer-related gene regulation
- Keywords
- HNF4α, enhancers, hepatocytes, histone modifications, H3K27ac, 5-hydroxymethylcytosine, DNA hydroxymethylation, TET3
- MeSH terms
- Animals, Cell Differentiation, Cells, Cultured, Female, Humans, Liver, Mice, Inbred C57BL
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