HBO1 functions as an epigenetic barrier to hepatocyte plasticity and reprogramming during liver injury
Open accessAbstract
Hepatocytes can reprogram into biliary epithelial cells (BECs) during liver injury, but the underlying epigenetic mechanisms remain poorly understood. Here, we define the chromatin dynamics of this process using single-cell ATAC-seq and identify YAP/TEAD activation as a key driver of chromatin remodeling. An in vivo CRISPR screen highlights the histone acetyltransferase HBO1 as a critical barrier to reprogramming. HBO1 is recruited by YAP to target loci, where it promotes histone H3 lysine 14 acetylation (H3K14ac) and engages the chromatin reader zinc-finger MYND-type containing 8 (ZMYND8) to suppress YAP/TEAD-driven transcription. Loss of HBO1 accelerates chromatin remodeling, enhances YAP binding, and enables a more complete hepatocyte-to-BEC transition. Our findings position HBO1 as an epigenetic brake that restrains YAP-mediated reprogramming, suggesting that targeting HBO1 may enhance hepatocyte plasticity for liver regeneration.
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Written from the paper’s full text.
TL;DR
HBO1 acts as an epigenetic brake on YAP/TEAD-driven hepatocyte-to-biliary reprogramming during liver injury. YAP recruits HBO1 to target loci, where HBO1 deposits H3K14ac and engages ZMYND8 to suppress YAP/TEAD transcription; HBO1 loss accelerates chromatin remodeling and enables a more complete transition.
Key findings
- scATAC-seq in DDC and YAP-driven models showed reprogrammed hepatocytes acquire BEC-like but incomplete chromatin accessibility; TEAD motifs were enriched, and YAP activation caused rapid chromatin changes by day 3 followed by gradual transition to BECs by day 28, with BEC-specific changes emerging before loss of hepatocyte accessibility.
- An in vivo CRISPR screen identified 13 other positive regulators and 8 negative regulators of YAP-driven reprogramming; five of five sgRNAs targeting Hbo1 were over-represented. HBO1 depletion increased hepatomegaly, clonal overgrowth, SOX9/CK19 expression, and accelerated YAP-mediated reprogramming, while HBO1 overexpression suppressed YAP-driven liver overgrowth and BEC reprogramming.
- HBO1 depletion abolished H3K14ac with marginal effect on H4K12ac; the catalytic-dead HBO1 E508Q mutant acted dominantly negative and potentiated YAP-driven phenotypes. YAP expression increased HBO1 occupancy at YAP-bound regions, and >75% of YAP binding sites overlapped HBO1-bound regions; HBO1 loss increased YAP and TEAD4 occupancy and YAP target gene expression.
- ZMYND8 was identified as a negative regulator; HBO1-driven inhibition of hepatomegaly after YAP activation was rescued by Zmynd8 loss, and Zmynd8 depletion increased H3K4me3 and YAP occupancy at target genes. In DDC injury, Hbo1 depletion caused a near 5-fold increase in hepatocyte-derived SOX9- or OPN-expressing cells; in MDA injury, HBO1 loss increased liver size and SOX9/OPN-expressing hepatocyte-lineage cells.
Methods
- Mouse models included 0.1% DDC diet for 6 weeks, MDA at 50 mg/kg four times every other day, TetO-YAP-S127A and Cre-dependent Cas9 alleles, AAV2/8-Cre lineage tracing, and single-cell ATAC-seq (sciATAC/dscATAC) across reprogramming time points from day 0 to day 28.
- The in vivo CRISPR screen used a Sleeping Beauty–integrated sgRNA library targeting epigenetic regulators, hydrodynamic tail-vein delivery, delayed tamoxifen, 6 weeks of doxycycline, sorting of EGFP+EPCAM+ cells, sgRNA sequencing, and STARS enrichment analysis.
- Bulk ATAC-seq, RNA-seq, ChIP-seq/ChIP-qPCR, co-immunoprecipitation, immunohistochemistry/immunofluorescence, and RNA FISH were analyzed with chromVAR, cisTopic, UMAP, Louvain clustering, GSEA, DESeq2, CUT&RUNTools, and deepTools.
Limitations
- Stated: further research is needed to translate these findings into clinically viable approaches, including development and use of small-molecule HBO1 inhibitors; findings are primarily based on murine models, so whether therapeutic HBO1 inactivation applies clinically remains to be determined.
- Evident: the in vivo screen used an intermediate-size library; the authors note that larger and more complex libraries (up to 10-fold) could be screened and that improved library design would allow more complex screens. No human validation is presented in the paper.
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Claims the paper makes
33 of 38 cited sources checked · 14 supported · 0 flagged · accuracy not yet measured
- Interpretationown data
Increased chromatin accessibility near YAP target genes suggests a pivotal role for YAP/TEAD signaling in the reprogramming process.
“Furthermore, increased chromatin accessibility near YAP target genes suggested a pivotal role for YAP/TEAD signaling in the reprogramming process (Figure S1C), supporting previous data10.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [10] Yimlamai D, Christodoulou C, Galli GG, Yanger K, Pepe-Mooney B, Gurung B, Shrestha K, Cahan P, Stanger BZ, and Camargo FD (2014). Hippo pathway activity influences liver cell fate. Cell 157, 1324– 1338. 10.1016/j.cell.2014.03.060. 24906150 PMC4136468 source
The Results sections on the liver progenitor program and NOTCH signaling support a role for YAP/TEAD in hepatocyte reprogramming: they report YAP-driven fate changes and YAP/TEAD binding and regulation of NOTCH-pathway genes. The paper reports chromatin occupancy, not increased chromatin accessibility near YAP target genes, so it does not support the specific observation used in the citing sentence. (LLM, conf=0.85)
Experimental — accuracy not yet measured
- Findingown data
Even at day 28, reprogrammed hepatocytes maintained distinct chromatin accessibility compared to BECs, despite resembling them morphologically and transcriptionally.
“Even at this later stage, reprogrammed hepatocytes maintained distinct chromatin accessibility compared to BECs (Figure 1H), despite resembling them morphologically and transcriptionally10 (Figure S1E).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [10] Yimlamai D, Christodoulou C, Galli GG, Yanger K, Pepe-Mooney B, Gurung B, Shrestha K, Cahan P, Stanger BZ, and Camargo FD (2014). Hippo pathway activity influences liver cell fate. Cell 157, 1324– 1338. 10.1016/j.cell.2014.03.060. 24906150 PMC4136468 source
- Premisecitation
ZMYND8 functions as a reader to recognize the acetylation of histone 3 at K14.
“ZMYND8 (also named PRKCBP1 or RACK7) functions as a reader to recognize the acetylation of histone 3 at K14.”
Quote in the paperSubstantial claim3 of 3 sources checked- cites [35] Gong F, and Miller KM (2018). Double duty: ZMYND8 in the DNA damage response and cancer. Cell Cycle 17, 414– 420. 10.1080/15384101.2017.1376150. 29393731 PMC5927707 source
- cites [36] Li N, Li Y, Lv J, Zheng X, Wen H, Shen H, Zhu G, Chen TY, Dhar SS, Kan PY, (2016). ZMYND8 Reads the Dual Histone Mark H3K4me1-H3K14ac to Antagonize the Expression of Metastasis-Linked Genes. Mol Cell 63, 470– 484. 10.1016/j.molcel.2016.06.035. 27477906 PMC4975651 source
- cites [37] Shen H, Xu W, Guo R, Rong B, Gu L, Wang Z, He C, Zheng L, Hu X, Hu Z, (2016). Suppression of Enhancer Overactivation by a RACK7-Histone Demethylase Complex. Cell 165, 331– 342. 10.1016/j.cell.2016.02.064. 27058665 PMC4826479 source
The Results section ('RACK7 primarily binds active enhancers'; page unavailable) identifies RACK7 as ZMYND8 and reports its binding at active enhancers. It describes the related protein BS69/ZMYND11—not RACK7—as a histone-mark reader. Searches for H3K14, lysine-14 acetylation, and acetylated-histone recognition found no passage saying that ZMYND8 reads H3K14 acetylation. (LLM, conf=0.86)
Experimental — accuracy not yet measured
- Findingown data
Single molecule FISH measurements for Amotl2 demonstrated increased expression of this transcript in Hbo1-depleted hepatocytes.
“Notably, single molecule FISH measurements for Amotl231, a well-known YAP target, demonstrated the increased expression of this transcript in Hbo1-depleted hepatocytes (Figure 4C).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [31] Yu FX, Zhao B, and Guan KL (2015). Hippo Pathway in Organ Size Control, Tissue Homeostasis, and Cancer. Cell 163, 811– 828. 10.1016/j.cell.2015.10.044. 26544935 PMC4638384 source
The cited review does not report single-molecule FISH measurements or increased Amotl2 expression in Hbo1-depleted hepatocytes; the citing sentence points to its own Figure 4C for that result. The review’s “Hippo Pathway in Early Embryonic Development” section mentions AMOT/AMOTL2 depletion in embryos, but does not address this measurement. Searches for Amotl2 and Hbo1-depleted hepatocytes found no supporting passage. (LLM, conf=0.76)
Experimental — accuracy not yet measured
- Premisecitation
Similar observations in humans suggest that hepatocyte-to-BEC conversion may play a role in conditions such as biliary obstruction and primary biliary cirrhosis.
“and similar observations in humans suggest that hepatocyte-to-BEC conversion may play a role in conditions such as biliary obstruction and primary biliary cirrhosis49.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [49] Limaye PB, Alarcon G, Walls AL, Nalesnik MA, Michalopoulos GK, Demetris AJ, and Ochoa ER (2008). Expression of specific hepatocyte and cholangiocyte transcription factors in human liver disease and embryonic development. Lab Invest 88, 865– 872. 10.1038/labinvest.2008.56. 18574450 PMC2631390 source
- Premisecitation
Lineage-tracing studies in animal models have confirmed that hepatocytes contribute to bile duct remodeling following cholangiocyte injury.
“Lineage-tracing studies in animal models have confirmed that hepatocytes contribute to bile duct remodeling following cholangiocyte injury10,43–48”
Quote in the paperSubstantial claim6 of 7 sources checked- cites [10] Yimlamai D, Christodoulou C, Galli GG, Yanger K, Pepe-Mooney B, Gurung B, Shrestha K, Cahan P, Stanger BZ, and Camargo FD (2014). Hippo pathway activity influences liver cell fate. Cell 157, 1324– 1338. 10.1016/j.cell.2014.03.060. 24906150 PMC4136468 source
The Results (no page supplied) report lineage tracing in mice showing that hepatocytes can form ductular structures after Hippo-pathway manipulation. The Discussion also reports lineage-tracing evidence of hepatocytes acquiring biliary features during injury. Neither passage establishes that hepatocytes contribute to bile duct remodeling specifically following cholangiocyte injury. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [43] Schaub JR, Huppert KA, Kurial SNT, Hsu BY, Cast AE, Donnelly B, Karns RA, Chen F, Rezvani M, Luu HY, (2018). De novo formation of the biliary system by TGFbeta-mediated hepatocyte transdifferentiation. Nature 557, 247– 251. 10.1038/s41586-018-0075-5. 29720662 PMC6597492 source
The Abstract (page unavailable) reports hepatocyte fate tracing in mice: after DDC-induced cholestatic liver injury, hepatocytes gave rise to cells in reactive ductules. It also reports that hepatocytes formed functional peripheral bile ducts in mice lacking those ducts. These findings support a hepatocyte contribution to biliary repair, but the paper does not establish that the reported remodeling followed cholangiocyte injury specifically. (LLM, conf=0.83)
Experimental — accuracy not yet measured - cites [44] Tarlow BD, Pelz C, Naugler WE, Wakefield L, Wilson EM, Finegold MJ, and Grompe M. (2014). Bipotential adult liver progenitors are derived from chronically injured mature hepatocytes. Cell Stem Cell 15, 605– 618. 10.1016/j.stem.2014.09.008. 25312494 PMC4254170 source
- cites [45] Yanger K, Zong Y, Maggs LR, Shapira SN, Maddipati R, Aiello NM, Thung SN, Wells RG, Greenbaum LE, and Stanger BZ (2013). Robust cellular reprogramming occurs spontaneously during liver regeneration. Genes & development 27, 719– 724. 10.1101/gad.207803.112. 23520387 PMC3639413 source
- cites [46] Merrell AJ, Peng T, Li J, Sun K, Li B, Katsuda T, Grompe M, Tan K, and Stanger BZ (2021). Dynamic Transcriptional and Epigenetic Changes Drive Cellular Plasticity in the Liver. Hepatology 74, 444– 457. 10.1002/hep.31704. 33423324 PMC8271088 source
- cites [47] Michalopoulos GK, Barua L, and Bowen WC (2005). Transdifferentiation of rat hepatocytes into biliary cells after bile duct ligation and toxic biliary injury. Hepatology 41, 535– 544. 10.1002/hep.20600. 15726663 PMC1821079 source
- cites [48] Katsuda T, Sussman JH, Ito K, Katznelson A, Yuan S, Takenaka N, Li J, Merrell AJ, Cure H, Li Q, (2024). Cellular reprogramming in vivo initiated by SOX4 pioneer factor activity. Nature communications 15, 1761. 10.1038/s41467-024-45939-z. PMC10897393 38409161 source
The Introduction (page unavailable) says hepatocytes can become biliary epithelial cells after liver injury and that the model permits tracing cells during this change. The Results section on Sox4 and Sox9 (page unavailable) documents hepatocyte reprogramming after DDC-induced cholestatic injury, but does not establish bile duct remodeling specifically following cholangiocyte injury. (LLM, conf=0.85)
Experimental — accuracy not yet measured
- Interpretationcitation
Through coordination of this and other epigenetics pathways, YAP activity is able to be amplified robustly to ensure a timely adjustment during liver injury and regeneration.
“Through coordination of this and other epigenetics pathways42, YAP activity is able to be amplified robustly to ensure a timely adjustment during liver injury and regeneration.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [42] Aloia L, McKie MA, Vernaz G, Cordero-Espinoza L, Aleksieva N, van den Ameele J, Antonica F, Font-Cunill B, Raven A, Aiese Cigliano R, (2019). Epigenetic remodelling licences adult cholangiocytes for organoid formation and liver regeneration. Nat Cell Biol 21, 1321– 1333. 10.1038/s41556-019-0402-6. 31685987 PMC6940196 source
The Results section (page not available in our copy) shows that TET1-mediated epigenetic regulation affects YAP/Hippo pathway components during the response to liver damage; the Discussion says this contributes to ductal-cell regeneration. The paper does not establish that coordination among multiple epigenetic pathways robustly amplifies YAP activity or ensures a timely adjustment. (LLM, conf=0.85)
Experimental — accuracy not yet measured
- Findingown data
Silencing of HBO1 further augmented YAP activity by examining Amotl2 transcripts.
“Silencing of HBO1 further augmented YAP activity by examining Amotl2 transcripts (Figure 4F).”
Quote in the paperSubstantial claim - Findingown data
Hepatocyte HBO1 overexpression increased H3K14 acetylation in vivo.
“Moreover, hepatocyte HBO1 overexpression increased H3K14 acetylation in vivo (Figure 3I and S3H).”
Quote in the paperSubstantial claim - Findingown data
Five out of five sgRNAs targeting Hbo1 were significantly over-represented in EGFP+ EPCAM+ cells.
“Among the top hits, five out of five sgRNAs targeting Hbo1 were significantly over-represented in EGFP+ EPCAM+ cells (Figure 2G).”
Quote in the paperSubstantial claim - Findingown data
The CRISPR screen identified 13 positive regulators and 8 negative regulators that inhibit or potentiate YAP-driven reprogramming upon depletion, respectively.
“In addition to YAP sgRNAs, we identified 13 other positive regulators and 8 negative regulators that inhibit or potentiate YAP-driven reprogramming upon depletion, respectively (Figure 2G).”
Quote in the paperSubstantial claim - Findingown data
HBO1-driven inhibition of hepatomegaly after YAP activation can be rescued by genetic loss of Zmynd8.
“Indeed, HBO1-driven inhibition of hepatomegaly after YAP activation can be rescued by the genetic loss of Zmynd8 (Figure 7A and 7B).”
Quote in the paperSubstantial claim - Findingown data
Acute YAP overexpression led to the up-regulation of Hbo1 mRNA and protein expression level.
“Furthermore, acute YAP overexpression led to the up-regulation of Hbo1 mRNA and protein expression level (Figure S7G and S7H), suggesting that Hbo1 is a direct target of YAP.”
Quote in the paperSubstantial claim - Findingown data
HBO1 depletion with YAP activation for 28 days led to a near complete loss of chromatin accessibility in many hepatocyte specific regulatory regions.
“On the other hand, HBO1 depletion with YAP activation for 28 days led to a near complete loss of chromatin accessibility in many hepatocyte specific regulatory regions (Figure 5D and S5F).”
Quote in the paperSubstantial claim - Findingown data
Bulk track analysis showed intervening chromatin accessibility around hepatic and biliary marker genes.
“Bulk track analysis corroborated these findings, showing intervening chromatin accessibility around hepatic and biliary marker genes (Figure S1B).”
Quote in the paperNot a substantial claim - Findingown data
ZMYND8 was identified as a negative regulator of YAP-driven reprogramming.
“In our screen results, the bromodomain protein zinc finger MYND-type containing 8 (ZMYND8) was also identified as a negative regulator of YAP-driven reprogramming (Figure 2G).”
Quote in the paperSubstantial claim - Findingown data
YAP and TEAD4 occupied DNA regions upstream of the Hbo1 gene through analysis of hepatocyte ChIP-seq results.
“We also found that YAP and TEAD4 occupied DNA regions upstream of the Hbo1 gene through analysis of hepatocyte ChIP-seq results (Figure S7E).”
Quote in the paperSubstantial claim - Findingown data
HBO1 depletion in YAP-expressing hepatocytes significantly potentiated the YAP transcriptional signature.
“HBO1 depletion in YAP-expressing hepatocytes significantly potentiated the YAP transcriptional signature (Figure 5H, 5I and S5I).”
Quote in the paperSubstantial claim - Findingown data
BEC-associated motifs were slightly depleted in Hbo1-depleted hepatocytes.
“If anything, BEC-associated motifs were slightly depleted in Hbo1-depleted hepatocytes (Figure S5B).”
Quote in the paperNot a substantial claim - Findingown data
HBO1 loss robustly surged the number of biliary marker SOX9 or OPN expressing cells derived from the GFP-labeled hepatocyte lineage.
“Moreover, HBO1 loss robustly surged the number of the biliary marker SOX9 or OPN expressing cells derived from the GFP-labeled hepatocyte lineage (Figure 4E).”
Quote in the paperSubstantial claim - Findingown data
Overexpression of HBO1 or HBO1 catalytic dead mutant E508Q did not affect YAP acetylation levels.
“However, overexpression of HBO1 or HBO1 catalytic dead mutant, HBO1 E508Q, did not affect YAP acetylation levels (Figure S6C).”
Quote in the paperSubstantial claim - Findingown data
In this genetic context, Zmynd8 depletion promoted Ki67, SOX9 and CK19 expression.
“In this genetic context, Zmynd8 depletion promoted Ki67, SOX9 and CK19 expression (Figure 7C and 7D).”
Quote in the paperSubstantial claim - Findingown data
ChIP-seq analyses demonstrate that HBO1 loss significantly increased YAP and TEAD4 occupancy across target genes.
“ChIP-seq analyses demonstrate that HBO1 loss significantly increased YAP and TEAD4 (Figure 6E, 6F and 6G) occupancy across target genes.”
Quote in the paperSubstantial claim - Findingown data
HBO1 depletion showed minimal effects on most TF motifs associated with hepatocyte and BEC identity at baseline.
“In general, HBO1 depletion showed minimal effects on most TF motifs associated with hepatocyte and BEC identity (Figure S5A).”
Quote in the paperSubstantial claim - Findingown data
In the absence of YAP overexpression, Zmynd8 depletion had no noticeable effect on cell proliferation or cell state.
“However, in the absence of YAP overexpression, Zmynd8 depletion had no noticeable effect on cell proliferation or cell state (Figures S7A–S7D).”
Quote in the paperSubstantial claim - Findingown data
YAP expression resulted in a significantly higher density of H3K14ac marks in YAP bound regions.
“Moreover, we find that YAP expression resulted in a significantly higher density of H3K14ac marks in YAP bound regions (Figure 6D and S6G).”
Quote in the paperSubstantial claim - Findingown data
HBO1-E508Q further potentiated YAP-driven effects in the liver.
“Thus, HBO1-E508Q, instead of a suppressive effect, further potentiated YAP-driven effects in the liver (Figure S3I-S3L).”
Quote in the paperSubstantial claim - Findingown data
BEC-specific changes in chromatin structure emerged earlier than the loss of hepatocyte chromatin accessibility features.
“Analysis of hepatic and biliary ID scores revealed that BEC-specific changes in chromatin structure emerged earlier than the loss of hepatocyte chromatin accessibility features (Figure 1I).”
Quote in the paperSubstantial claim - Findingown data
Following low dose Dox for one week to induce YAP expression, hepatocyte-derived BECs are observed to be arranged and form new bile ducts after long-term regeneration in MDA-injured and Hbo1 depleted liver.
“Remarkably, following the addition of low dose of Dox for one week to induce YAP expression, hepatocyte-derived BECs are observed to be arranged and form new bile ducts after long-term regeneration in MDA-injured and Hbo1 depleted liver (Figure 4G, 4H and 4I).”
Quote in the paperSubstantial claim - Findingown data
Co-immunoprecipitation analyses showed YAP interacted with HBO1 endogenously.
“Indeed, co-immunoprecipitation analyses showed YAP interacted with HBO1 endogenously (Figure 6A and S6B).”
Quote in the paperSubstantial claim - Findingown data
There was a near 5-fold increase in the number of hepatocyte-derived cells expressing SOX9 or Osteopontin (OPN) in Hbo1-depleted cells.
“We found a near 5-fold increase in the number of hepatocyte-derived cells expressing the ductal marker SOX9 or Osteopontin (OPN) in Hbo1-depleted cells (Figure 4B and Figure S4B).”
Quote in the paperSubstantial claim - Findingown data
HBO1 depletion reduced the H3K14ac mark in YAP target genes.
“As expected, HBO1 depletion reduced the H3K14ac mark in YAP target genes (Figure S6F).”
Quote in the paperSubstantial claim - Findingown data
HBO1 depletion in control hepatocytes displayed negligible effects on YAP and TEAD4 recruitment.
“HBO1 depletion in control hepatocytes displayed negligible effects on YAP and TEAD4 recruitment (Figure S6H), supporting our previous observation that HBO1 functions predominantly in a YAP-dependent manner.”
Quote in the paperNot a substantial claim - Findingown data
Similar to YAP, H3K14ac marked both promoter regions and distal regulatory elements.
“Similar to YAP, H3K14ac marked both promoter regions and distal regulatory elements (Figure S6D).”
Quote in the paperNot a substantial claim - Findingown data
HBO1-E508Q exhibited a dominant-negative effect on H3K14ac levels in vivo.
“Functionally, however, this mutant exhibited a dominant-negative effect on H3K14ac levels in vivo (Figure S3J).”
Quote in the paperSubstantial claim - Findingown data
TF motif analysis identified robust enrichment of the binding motifs of TEAD factors.
“We identified a robust enrichment of the binding motifs of TEAD factors (Figure 1E).”
Quote in the paperSubstantial claim - Findingown data
HBO1 loss robustly induced the expression of biliary, YAP target and cell cycle related genes.
“Moreover, HBO1 loss robustly induced the expression of biliary, YAP target and cell cycle related genes.”
Quote in the paperSubstantial claim - Findingown data
YAP expression induced a significant increase of HBO1 occupancy in YAP-bound regions but not non-YAP bound regions.
“Moreover, YAP expression induced a significant increase of HBO1 occupancy in YAP-bound regions but not non-YAP bound regions (Figure 6C).”
Quote in the paperSubstantial claim - Findingown data
Analysis of TF motifs associated with cell fate identity displayed no evidence of ongoing BEC reprogramming in Hbo1-depleted hepatocytes.
“Furthermore, analysis of TF motifs associated with cell fate identity displayed no evidence of ongoing BEC reprogramming (Figure S5A).”
Quote in the paperSubstantial claim - Findingown data
In the absence of YAP overexpression, HBO1 depletion showed no obvious effects on cell proliferation or cell state.
“Moreover, in the absence of YAP overexpression, HBO1 depletion showed no obvious effects on cell proliferation or cell state (Figure S5C, and S5D).”
Quote in the paperSubstantial claim - Findingown data
ChIP-seq in murine hepatocytes revealed that >75% of YAP binding sites overlapped with HBO1-bound regions after transgenic YAP activation.
“Indeed, chromatin immunoprecipitation coupled sequencing (ChIP-seq) in murine hepatocytes (Figure 6B) revealed that >75% of YAP binding sites overlapped with HBO1-bound regions (Figure S6E) after transgenic YAP activation.”
Quote in the paperSubstantial claim - Premisecitation
Adult hepatocytes can undergo reprogramming to give rise to functional biliary epithelial cells (BECs) and ductal progenitors under certain conditions.
“This is particularly true for adult hepatocytes, which under certain conditions undergo reprogramming to give rise to functional biliary epithelial cells (BECs) and ductal progenitors.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [8] Gadd VL, Aleksieva N, and Forbes SJ (2020). Epithelial Plasticity during Liver Injury and Regeneration. Cell Stem Cell 27, 557– 573. 10.1016/j.stem.2020.08.016. 32971004 source
- cites [9] Li W, Li L, and Hui L. (2020). Cell Plasticity in Liver Regeneration. Trends in cell biology 30, 329– 338. 10.1016/j.tcb.2020.01.007. 32200807 source
- Interpretationown data
The analysis robustly identified functional epigenetic mediators of the hepatocyte to BEC transition driven by YAP.
“Thus, our analysis robustly identified functional epigenetic mediators of the hepatocyte to BEC transition driven by YAP.”
Quote in the paperSubstantial claim - Interpretationown data
Hepatocyte-derived BECs retain partial features of chromatin accessibility from hepatocytes.
“indicating that hepatocyte-derived BECs retain partial features of chromatin accessibility from hepatocytes.”
Quote in the paperSubstantial claim - Interpretationown data
YAP drives an extensive, gradual, synchronous, but incomplete, set of changes in the chromatin state to reprogram mature hepatocytes to BECs.
“Taken together, our data indicate that YAP drives an extensive, gradual, synchronous, but incomplete, set of changes in the chromatin state to reprogram mature hepatocytes to BECs.”
Quote in the paperSubstantial claim - Interpretationown data
Functional and genetic data speak to a major role for HBO1 as a regulator of YAP-driven hepatocyte reprogramming.
“Thus, our functional and genetic data speak to a major role for HBO1 as a regulator of YAP-driven hepatocyte reprogramming.”
Quote in the paperSubstantial claim - Interpretationown data
HBO1 represents an epigenetic barrier for reprogramming in the context of YAP activation.
“Collectively, our results strongly support the idea that HBO1 represents an epigenetic barrier for reprogramming in the context of YAP activation.”
Quote in the paperSubstantial claim - Interpretationown data
Hbo1 is a direct target of YAP.
“suggesting that Hbo1 is a direct target of YAP.”
Quote in the paperSubstantial claim - Interpretationown data
HBO1-dependent H3K14 acetylation is the major chromatin modification deposited by HBO1 in the liver.
“Thus, our results imply that HBO1-dependant H3K14 acetylation is the major chromatin modification that is deposited by HBO1 in the liver.”
Quote in the paperSubstantial claim - Interpretationown data
Reprogrammed cells are in a transitional state between hepatic and biliary cell fates.
“Collectively, our data suggest that reprogrammed cells are in a transitional state between hepatic and biliary cell fates.”
Quote in the paperSubstantial claim - Interpretationown data
HBO1 antagonizes YAP-driven hepatocyte reprogramming through promoting acetylation of histone 3 at K14.
“Taken together, our data indicate that HBO1 antagonizes YAP-driven hepatocyte reprogramming through promoting acetylation of histone 3 at K14.”
Quote in the paperSubstantial claim - Interpretationown data
HBO1 suppresses YAP-mediated proliferation and reprogramming through the recruitment of ZMYND8 and the reduction of H3K4me3.
“These findings suggest that HBO1 suppresses YAP-mediated proliferation and reprogramming through the recruitment of ZMYND8 and the reduction of H3K4me3.”
Quote in the paperSubstantial claim - Interpretationown data
HBO1 has a critical role in controlling hepatocyte plasticity through regulation of YAP activity during physiological liver regeneration.
“These data speak to a critical role of HBO1 in controlling hepatocyte plasticity through regulation of YAP activity during physiological liver regeneration.”
Quote in the paperSubstantial claim - Interpretationreasoning
Once repairing is finished, YAP activity is rapidly turned down, thereby maintaining tissue homeostasis.
“Once the repairing is finished, YAP activity is rapidly turned down, thereby maintaining tissue homeostasis.”
Quote in the paperNot a substantial claim - Premisecitation
Under conditions where endogenous repair mechanisms are insufficient, hepatocytes can undergo reprogramming into biliary epithelial cells (BECs) to restore bile duct architecture.
“However, under conditions where endogenous repair mechanisms are insufficient, hepatocytes can undergo reprogramming into biliary epithelial cells (BECs) to restore bile duct architecture.”
Quote in the paperSubstantial claim - Study design and conductown data
Experiments with positive and negative controls corroborated the viability of the screening platform.
“Experiments with positive and negative controls corroborated the viability of our screening platform (Figure S2D, S2E and S2F).”
Quote in the paperSubstantial claim - Study design and conductreasoning
Under the experimental settings, only cells that have stably integrated sgRNA:CreER plasmids are able to express Cas9-EGFP upon TAM delivery and YAP-S127A after Dox administration.
“Under these experimental settings, only cells that have stably integrated sgRNA:CreER plasmids are able to express Cas9-EGFP upon TAM delivery and YAP-S127A after Dox administration.”
Quote in the paperSubstantial claim - Study design and conductown data
The screen hits were validated by assessing the consequences of individual sgRNA-mediated knockouts in vivo.
“We validated our hits by assessing the consequences of individual sgRNA-mediated knockouts in vivo (Figure 2H, 2I and Figure S2H).”
Quote in the paperSubstantial claim
- Classified as probably not a substantial claim. 25
- May combine two claims. 31
Classified as probably not a substantial claim.
PremisecitationAcute YAP overexpression results in hepatocyte reprogramming into BEC.
“Acute YAP overexpression results in hepatocyte reprogramming into BEC10.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [10] Yimlamai D, Christodoulou C, Galli GG, Yanger K, Pepe-Mooney B, Gurung B, Shrestha K, Cahan P, Stanger BZ, and Camargo FD (2014). Hippo pathway activity influences liver cell fate. Cell 157, 1324– 1338. 10.1016/j.cell.2014.03.060. 24906150 PMC4136468 source
In Results, under “YAP activation de-differentiates single adult hepatocytes” (page unavailable), lineage tracing shows that YAP induction gives hepatocytes ductal markers and a ductal/progenitor-like fate. The paper does not establish that acute overexpression converts them into mature biliary epithelial cells: many cells at one week retained a hepatocyte marker, and the reported fate change progressed over weeks. (LLM, conf=0.85)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationYAP predominantly exerts its transcriptional functions through interaction with the TEAD family of transcription factors.
“YAP predominantly exerts its transcriptional functions through interaction with the TEAD family of transcription factors, thereby promoting the expression of target genes12,13.”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites [12] Wu S, Liu Y, Zheng Y, Dong J, and Pan D. (2008). The TEAD/TEF family protein Scalloped mediates transcriptional output of the Hippo growth-regulatory pathway. Developmental cell 14, 388– 398. 10.1016/j.devcel.2008.01.007. 18258486 source
The Introduction reports that YAP interacts with TEAD/TEF transcription factors, and the Discussion suggests that the growth-regulatory activity of the fly Sd–Yki complex is conserved in mammals. The paper does not establish that YAP uses TEAD for *most* of its transcriptional functions; it also names other YAP-interacting transcription factors. Page numbers are unavailable in our copy. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [13] Zhang L, Ren F, Zhang Q, Chen Y, Wang B, and Jiang J. (2008). The TEAD/TEF family of transcription factor Scalloped mediates Hippo signaling in organ size control. Developmental cell 14, 377– 387. 10.1016/j.devcel.2008.01.006. 18258485 PMC2292673 source
Classified as probably not a substantial claim. May combine two claims.
PremisecitationYAP is necessary and sufficient for hepatocyte reprogramming into ductal cells.
“YAP, the main transducer of the Hippo pathway, has been reported to be necessary and sufficient for hepatocyte reprogramming into ductal cells10,11.”
Quote in the paperSubstantial claim2 of 2 sources checked- cites [10] Yimlamai D, Christodoulou C, Galli GG, Yanger K, Pepe-Mooney B, Gurung B, Shrestha K, Cahan P, Stanger BZ, and Camargo FD (2014). Hippo pathway activity influences liver cell fate. Cell 157, 1324– 1338. 10.1016/j.cell.2014.03.060. 24906150 PMC4136468 source
The Results section, “YAP activation de-differentiates single adult hepatocytes” (page unavailable), explicitly says high YAP levels are sufficient to impose a ductal/progenitor-like fate on adult hepatocytes. The passages found do not establish that YAP is necessary for hepatocyte-to-ductal reprogramming; the loss-of-function result in “NOTCH signaling downstream of YAP during reprogramming” concerns NOTCH signaling, not YAP. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [11] Monroe TO, Hill MC, Morikawa Y, Leach JP, Heallen T, Cao S, Krijger PHL, de Laat W, Wehrens XHT, Rodney GG, and Martin JF (2019). YAP Partially Reprograms Chromatin Accessibility to Directly Induce Adult Cardiogenesis In Vivo. Developmental cell 48, 765– 779 e767. 10.1016/j.devcel.2019.01.017. 30773489 PMC6435425 source
The Introduction identifies YAP as a Hippo-pathway effector, supporting that background part of the sentence. The Discussion section on YAP, ploidy and cell-cycle progression mentions hepatocyte proliferation, but neither it nor the other passages found addresses whether YAP is necessary and sufficient to reprogram hepatocytes into ductal cells. No page numbers were available in our copy. (LLM, conf=0.82)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationLoss of Nf2 or Lats1/2 forces hepatocytes to commit to the BEC lineage.
“Additionally, loss of Nf2 or Lats1/2 forces hepatocytes to commit to the BEC lineage14,15.”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [14] Lee DH, Park JO, Kim TS, Kim SK, Kim TH, Kim MC, Park GS, Kim JH, Kuninaka S, Olson EN, (2016). LATS-YAP/TAZ controls lineage specification by regulating TGFβ signaling and Hnf4α expression during liver development. Nature communications 7, 11961. 10.1038/ncomms11961. PMC4931324 27358050 source
The Results section, “Lats1/2 deletion triggers transition of hepatocytes to BECs” (page unavailable), reports that roughly 60% of immature BECs arose from Lats1/2-deficient hepatocytes via de-differentiation. This supports the Lats1/2 part, although “forces hepatocytes” is broader than the reported finding. The Methods mention Nf2 mice, but the passages found do not show that Nf2 loss causes this transition. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [15] Zhang N., Bai H., David KK., Dong J., Zheng Y., Cai J., Giovsnnini M., Liu P., Anders RA., and Pan D. (2010). The Merlin/NF2 tumor suppressor functions through the YAP oncoprotein to regulate tissue homeostasis in mammals. Developmental cell 19, 27– 38. 10.1016/j.devcel.2010.06.015. 20643348 PMC2925178 source
The Results section, “Loss of NF2 leads to hepatocyte and biliary epithelium overproliferation” (page unavailable), reports excess BECs after Nf2 deletion, but describes the proliferating cells as being of biliary origin; it does not show hepatocytes committing to the BEC lineage. The Results section, “NF2 is required for Hippo signaling” (page unavailable), reports reduced Lats1/2 activity in Nf2-deficient livers, not the effect of deleting Lats1/2. (LLM, conf=0.86)
Experimental — accuracy not yet measured
May combine two claims.
PremisecitationZMYND8 occupies many active enhancers and recruits KDM5C to super enhancer regions to maintain low H3K4me3 levels resulting in repression of enhancer activity.
“ZMYND8 occupies many active enhancers and recruits KDM5C to super enhancer regions to maintain low H3K4me3 levels resulting in the repression of enhancer activity 35–37.”
Quote in the paperSubstantial claim3 of 3 sources checked- cites [35] Gong F, and Miller KM (2018). Double duty: ZMYND8 in the DNA damage response and cancer. Cell Cycle 17, 414– 420. 10.1080/15384101.2017.1376150. 29393731 PMC5927707 source
- cites [36] Li N, Li Y, Lv J, Zheng X, Wen H, Shen H, Zhu G, Chen TY, Dhar SS, Kan PY, (2016). ZMYND8 Reads the Dual Histone Mark H3K4me1-H3K14ac to Antagonize the Expression of Metastasis-Linked Genes. Mol Cell 63, 470– 484. 10.1016/j.molcel.2016.06.035. 27477906 PMC4975651 source
The Results (page unavailable) show that ZMYND8 and JARID1D cooperate to repress metastasis-linked genes: ZMYND8 knockdown reduced JARID1D occupancy and increased H3K4me3 at those genes. The Discussion (page unavailable) suggests ZMYND8 may help recruit JARID1D. These passages do not establish recruitment of KDM5C to super-enhancer regions or repression of enhancer activity. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [37] Shen H, Xu W, Guo R, Rong B, Gu L, Wang Z, He C, Zheng L, Hu X, Hu Z, (2016). Suppression of Enhancer Overactivation by a RACK7-Histone Demethylase Complex. Cell 165, 331– 342. 10.1016/j.cell.2016.02.064. 27058665 PMC4826479 source
May combine two claims.
Findingown dataGSEA showed that upon YAP expression, HBO1-depletion induced significant positive enrichment of a BEC signature and negative enrichment of a hepatocyte signature.
“Moreover, GSEA analysis showed that upon YAP expression, HBO1-depletion induced significant positive enrichment of a BEC signature16 and negative enrichment of a hepatocyte signature (Figure S5J).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [16] Pepe-Mooney BJ, Dill MT, Alemany A, Ordovas-Montanes J, Matsushita Y, Rao A, Sen A, Miyazaki M, Anakk S, Dawson PA, (2019). Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration. Cell Stem Cell 25, 23– 38 e28. 10.1016/j.stem.2019.04.004. 31080134 PMC6814390 source
May combine two claims.
Findingown dataSingle cell molecule FISH of YAP target genes Cyr61 and Amotl2 validated their dramatically higher expression in vivo in the absence of HBO1 and their attenuation following HBO1 overexpression.
“Single cell molecule FISH of YAP target genes, Cyr61 and Amotl231, validated their dramatically higher expression in vivo in the absence of HBO1 (Figure 5F, 5G and S5G, and their attenuation following HBO1 overexpression (Figure S5H).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [31] Yu FX, Zhao B, and Guan KL (2015). Hippo Pathway in Organ Size Control, Tissue Homeostasis, and Cancer. Cell 163, 811– 828. 10.1016/j.cell.2015.10.044. 26544935 PMC4638384 source
The citation is attached to the identification of Cyr61 and Amotl2 as YAP target genes, not to the citing authors’ FISH results. The review’s ‘YAP/TAZ and Yki as Major Effectors of Hippo Signaling’ section discusses YAP target genes generally but does not identify Cyr61 or Amotl2 as targets. Searches for those genes and HBO1 found no passage supporting the specific claim; the review mentions AMOTL2 in a different context, as a Hippo-pathway component. (LLM, conf=0.78)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationPublished ChIP-seq datasets reveal a similar phenomenon in human cancer cell lines.
“Consistently, published ChIP-seq datasets34,38,39 reveal a similar phenomenon in human cancer cell lines (Figure S7F).”
Quote in the paperNot a substantial claim3 of 3 sources checked- cites [34] Galli GG, Carrara M, Yuan WC, Valdes-Quezada C, Gurung B, Pepe-Mooney B, Zhang T, Geeven G, Gray NS, de Laat W, (2015). YAP Drives Growth by Controlling Transcriptional Pause Release from Dynamic Enhancers. Mol Cell 60, 328– 337. 10.1016/j.molcel.2015.09.001. 26439301 PMC4624327 source
- cites [38] Stein C, Bardet AF, Roma G, Bergling S, Clay I, Ruchti A, Agarinis C, Schmelzle T, Bouwmeester T, Schubeler D, and Bauer A. (2015). YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers. PLoS Genet 11, e1005465. 10.1371/journal.pgen.1005465. 26295846 PMC4546604 source
- cites [39] Zanconato F, Forcato M, Battilana G, Azzolin L, Quaranta E, Bodega B, Rosato A, Bicciato S, Cordenonsi M, and Piccolo S. (2015). Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth. Nat Cell Biol 17, 1218– 1227. 10.1038/ncb3216. 26258633 PMC6186417 source
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductcitationFor the histone mark H3K14ac, the recommended histone ChIP-seq normalization pipeline was used to generate scale factors.
“For the histone mark H3K14ac, we used the recommended histone ChIP-seq normalization pipeline64 to generate scale factors.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [64] Jin H, Kasper LH, Larson JD, Wu G, Baker SJ, Zhang J, and Fan Y. (2020). ChIPseqSpikeInFree: a ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in. Bioinformatics (Oxford, England) 36, 1270– 1272. 10.1093/bioinformatics/btz720. 31566663 PMC7523640 source
Classified as probably not a substantial claim.
Study design and conductcitationTAM delivery was delayed by 3 weeks post-hydrodynamic injection until loss of episomal plasmids occurred.
“In order to ensure that sgRNA-mediated knockout only occurred in hepatocytes carrying an integrated plasmid cassette, TAM delivery was delayed by 3 weeks post-hydrodynamic injection until loss of episomal plasmids occurred25.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [25] Bell JB, Aronovich EL, Schreifels JM, Beadnell TC, and Hackett PB (2010). Duration of expression and activity of Sleeping Beauty transposase in mouse liver following hydrodynamic DNA delivery. Mol Ther 18, 1796– 1802. 10.1038/mt.2010.152. 20628359 PMC2951564 source
The section on SB transposase gene loss reports that plasmid copy number fell by 90% over the first two weeks after hydrodynamic delivery, supporting a substantial decline by three weeks. It also says the remaining 10% stabilized, so the paper does not establish complete loss of episomal plasmids or that waiting three weeks ensures activity only in hepatocytes with an integrated cassette. The paper does not study TAM delivery. (LLM, conf=0.88)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationUnder physiological conditions, activation of YAP is necessary and sufficient to reprogram hepatocytes and to precisely control developmental outcomes, organ size and tissue repair.
“Under physiological conditions, activation of YAP is necessary and sufficient to not only reprogram hepatocytes but to precisely control developmental outcomes, organ size and tissue repair10,16,40,41.”
Quote in the paperNot a substantial claim3 of 4 sources checked- cites [10] Yimlamai D, Christodoulou C, Galli GG, Yanger K, Pepe-Mooney B, Gurung B, Shrestha K, Cahan P, Stanger BZ, and Camargo FD (2014). Hippo pathway activity influences liver cell fate. Cell 157, 1324– 1338. 10.1016/j.cell.2014.03.060. 24906150 PMC4136468 source
The Results section, “YAP activation de-differentiates single adult hepatocytes” (page not supplied), reports that high levels of YAP are sufficient to impose a progenitor-like fate on adult hepatocytes. It does not establish that YAP activation is necessary for reprogramming under physiological conditions. The Discussion (page not supplied) describes a possible role in liver repair, rather than demonstrating precise control of developmental outcomes, organ size, and tissue repair. (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites [16] Pepe-Mooney BJ, Dill MT, Alemany A, Ordovas-Montanes J, Matsushita Y, Rao A, Sen A, Miyazaki M, Anakk S, Dawson PA, (2019). Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration. Cell Stem Cell 25, 23– 38 e28. 10.1016/j.stem.2019.04.004. 31080134 PMC6814390 source
The Results section ('YAP is Essential in Hepatocytes for the Regenerative Ductular Response to Injury'; page not provided) shows that deleting YAP impairs hepatocyte reprogramming and the regenerative response after DDC injury. The Discussion reports that overexpression of active YAP drives reprogramming, citing earlier work. This does not establish necessity and sufficiency under physiological conditions, or precise control of developmental outcomes and organ size; the Results also report no detectable high-YAP signature in homeostatic hepatocytes. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [40] Moya IM, and Halder G. (2019). Hippo-YAP/TAZ signalling in organ regeneration and regenerative medicine. Nature reviews. Molecular cell biology 20, 211– 226. 10.1038/s41580-018-0086-y. 30546055 source
The sections ‘YAP promotes dedifferentiation and stemness’ and ‘YAP activation and liver regeneration’ report that experimental YAP overexpression reprogrammed mouse hepatocytes into progenitor-like cells and enhanced liver repair. They do not establish that YAP activation is necessary for hepatocyte reprogramming under physiological conditions. The sections on growth and regeneration describe tissue-specific effects, not precise control of developmental outcomes, organ size and repair; liver regeneration was delayed, but not prevented, when Yap and Taz were deleted. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [41] Varelas X. (2014). The Hippo pathway effectors TAZ and YAP in development, homeostasis and disease. Development (Cambridge, England) 141, 1614– 1626. 10.1242/dev.102376. 24715453 source
May combine two claims.
Findingown datascATAC-seq analysis unveiled major differences in chromatin landscape between hepatocytes and BECs, whereas DDC-induced reprogrammed hepatocytes exhibited overlapping chromatin accessibility with BECs.
“scATAC-seq analysis unveiled major differences in chromatin landscape between hepatocytes and BECs, whereas DDC-induced reprogrammed hepatocytes exhibited overlapping chromatin accessibility with BECs (Figure 1B and 1C).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataQuantifying reprogramming using hepatic and biliary ID scores indicated a gradual transition from clusters 1 to cluster 4, with reprogrammed cells showing intermediate scores.
“Quantifying reprogramming using hepatic and biliary ID scores (see Methods) indicated a gradual transition from clusters 1 to cluster 4, with reprogrammed cells showing intermediate scores (Figure 1D).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataIn the presence of Dox for two weeks, Hbo1 depletion promoted earlier SOX9 and panCK expression, indicating that Hbo1 depletion accelerates YAP-mediated reprogramming.
“In the presence of Dox for two weeks, Hbo1 depletion promoted earlier SOX9 and panCK expression, indicating that Hbo1 depletion accelerates YAP-mediated reprogramming (Figure 3E).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataDepletion of HBO1 in hepatocytes significantly reduced H3K14 acetylation and increased liver size in the MDA model.
“Compared with control, depletion of HBO1 in hepatocytes significantly reduced the level of H3K14 acetylation (Figure S4C) and increased the liver size (Figure 4D).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataLoss of HBO1 specifically in hepatocytes resulted in loss of H3K14 acetylation and significant augmentation of the ductular reaction post-DDC as measured by increased panCK positive cells.
“Compared with control, loss of HBO1 specifically in hepatocytes resulted in a loss of H3K14 acetylation (Figure S4A) and led to significant augmentation of the ductular reaction post-DDC as measured by increased panCK positive cells (Figure 4A).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataCompared with control, YAP-induced chromatin accessibility changes proceeded with faster dynamics in the context of HBO1 depletion, including gain of chromatin accessibility in biliary specific genes, YAP target genes and cell cycle related genes, while concurrently loss of chromatin accessibility of hepatic genes.
“Again, compared with control, YAP-induced chromatin accessibility changes proceeded with faster dynamics in the context of HBO1 depletion, including gain of chromatin accessibility in biliary specific genes, YAP target genes and cell cycle related genes, while concurrently loss of chromatin accessibility of hepatic genes (Figure 5H and 5I).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataOverexpression of Hbo1 led to near complete suppression of YAP-driven liver overgrowth, decreased hepatocyte proliferation, and diminished BEC reprogramming.
“Conversely, overexpression of Hbo1 using a transposon construct led to a near complete suppression of YAP-driven liver overgrowth (Figure 3F and 3G), decreased hepatocyte proliferation, and diminished BEC reprogramming (Figure 3H, 3I, S3B, S3C, S3D and S3E).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataChIP-qPCR studies demonstrate that Zmynd8 depletion significantly increases the levels of H3K4me3 and the occupancy of YAP at target genes.
“Furthermore, ChIP-qPCR studies demonstrate that Zmynd8 depletion significantly increases the levels of H3K4me3 and the occupancy of YAP at target genes (Figure 7E).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataHBO1 depletion enhanced and accelerated accessibility of YAP target genes and BEC specific genes during reprogramming.
“Notably, examination of the chromatin landscape in a number of representative regions revealed that HBO1 depletion enhanced and accelerated accessibility of YAP target genes (Figure 5B and S5E) and BEC specific genes (Figure 5C) during reprogramming.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataIndividual transposon sgRNA-mediated knockout of Hbo1 in combination with YAP overexpression led to major hepatomegaly phenotypes and clonal overgrowth.
“Individual transposon sgRNA-mediated knockout of Hbo1 in combination with YAP overexpression led to major hepatomegaly phenotypes (Figure 3A and B) and clonal overgrowth (Figure 2I).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataAnalysis revealed rapid chromatin changes by day 3 post-YAP activation, followed by a gradual transition to BECs by day 28.
“Our analysis revealed rapid chromatin changes by day 3 post-YAP activation, followed by a gradual transition to BECs by day 28.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataHbo1 knockout clones exhibited increased proliferative indices and biliary molecular features indicated by expression of SOX9 and CK19.
“Hbo1 knockout clones exhibited increased proliferative indices and biliary molecular features indicated by the expression of SOX9 and CK19 (early and late reprogramming markers, respectively) (Figure 3C and Figure S3A).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataHBO1 depletion dramatically abolished H3K14ac but displayed marginal effect on H4K12ac in liver samples and in a cholangiocarcinoma cell line.
“We found that HBO1 depletion dramatically abolished H3K14ac but displayed marginal effect on H4K12ac in liver samples and in a cholangiocarcinoma cell lines (Figure 3J, S3F and S3G).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataGlobal transcriptome analysis revealed that HBO1 depletion only displayed some hepatocyte and BEC identity genes changes with no significant trends toward any cell fate transitions.
“Global transcriptome analysis revealed that HBO1 depletion only displayed some hepatocyte and BEC identity genes changes with no significant trends toward any cell fate transitions.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThe screen hits include histone acetyltransferases Tip60, Mof, Moz and Hbo1, lysine methyltransferases Setd1b, Setdb1, Setd8, Dot1l, Ehmt1 and Ehmt2, lysine demethylases Kdm6a and Phf8, histone deacetylase Sirt1, and bromodomain-containing proteins Brd1 and Zmynd8.
“Our hits include histone acetyltransferases (Tip60, Mof, Moz and Hbo1), lysine methyltransferases (Setd1b, Setdb1, Setd8, Dot1l, Ehmt1 and Ehmt2), lysine demethylases (Kdm6a, and Phf8), histone deacetylases (Sirt1), and bromodomain-containing proteins (Brd1 and Zmynd8).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataAggregated scATAC-seq track data confirmed opening of chromatin at regulatory regions of BEC-specific genes, while minimal changes were noted in regulatory regions surrounding hepatocyte-specific genes even 28 days after YAP induction.
“Aggregated scATAC-seq track data confirmed the opening of chromatin at regulatory regions of BEC-specific genes, while minimal changes were noted in regulatory regions surrounding hepatocyte-specific genes, even 28 days after YAP induction (Figure 1J)”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataGlobal analysis of TF motifs showed more rapid and profound changes in chromatin accessibility upon HBO1 depletion, leading to an epigenetic state that more closely resembles bona fide BECs.
“This accelerated and enhanced reprogramming was corroborated by the global analysis of TF motifs, where we again observed more rapid and profound changes in chromatin accessibility (Figure 5E), leading to an epigenetic state that more closely resembles bona fide BECs.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataEnrichment of JUN/FOS, NFκB and BACH2 transcription factor motifs strongly increased as cells reprogram, while binding motifs of LEF1/TCF7L2 factors related to Wnt signaling displayed reduced accessibility.
“For instance, enrichment of motifs of JUN/FOS, NFκB and BACH2 transcription factor are strongly increased as cells reprogram, while the binding motifs of LEF1/TCF7L2 factors related to Wnt signaling display reduced accessibility (Figure 1F).”
Quote in the paperNot a substantial claimMay combine two claims.
Interpretationown dataYAP-mediated HBO1 induction and recruitment form a negative feedback loop to self-regulate its own transcriptional outputs and control the hepatocyte-to-BEC fate transition.
“Together with our previous results, these data speak to a model where YAP-mediated HBO1 induction and recruitment form a negative feedback loop to self-regulate its own transcriptional outputs and control the hepatocyte-to-BEC fate transition.”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationown dataHBO1 participates in YAP-driven reprogramming and regeneration through the alteration of both chromatin landscape and transcriptome.
“Collectively, these data indicate that HBO1 participates in YAP-driven reprogramming and regeneration through the alteration of both chromatin landscape and transcriptome.”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationreasoningHBO1 functions as an epigenetic 'brake' for YAP functions and hepatocyte reprogramming.
“In this context, we posit HBO1 functions as an epigenetic ‘brake’ for YAP functions and hepatocyte reprogramming (Figure 7F).”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenThe number of PCR cycles was optimized by DNA quantification to stop in the middle of the linear amplification phase.
“The number of cycles was optimized by DNA quantification to stop in the middle of the linear amplification phase.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Interpretationown dataSince the findings are primarily based on murine models, it remains to be determined whether therapeutic inactivation of HBO1 can be successfully applied in clinical settings.
“Additionally, since our findings are primarily based on murine models, it remains to be determined whether the therapeutic inactivation of HBO1 can be successfully applied in clinical settings.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenTranscription factors YAP, TEAD4, and HBO1 were normalized using equal background normalization.
“Transcription factors YAP, TEAD4, HBO1 adopted equal background normalization.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenThe average of technical replicates was used to represent the value of each biological replicate.
“The average of technical replicates was used to represent the value of each biological replicate.”
Quote in the paperNot a substantial claimMay combine two claims.
Interpretationnone givenYAP-mediated HBO1 induction and recruitment promote acetylation of H3 at K14 and engage ZMYND8 to restrict its own transcriptional output.
“Here, we elucidate mechanisms by which YAP-mediated HBO1 induction and recruitment promote the acetylation of H3 at K14 and engage ZMYND8 to restrict its own transcriptional output.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim.
Study design and conductreasoningNormalizing ChIP-seq samples according to the described procedure enables comparison between Dox(−) and Dox(+) samples.
“To enable a comparison between Dox (−) and Dox (+) samples, we normalized the samples according to the following procedure.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataApproximately 70-95% of high quality reads contained the sgRNA scaffold inside the amplified region.
“Approximately 70–95% of high quality reads contained the sgRNA scaffold inside the amplified region and were extracted from the raw fasta files using grep (sgRNA specific reads).”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim.
Study design and conductnone givenStatistical analysis was performed on biological replicates to compare control and treatment groups.
“Statistical analysis was performed on biological replicates to compare control and treatment groups.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductreasoningAt least 2000-fold colonies per sgRNA clone were recovered in each transformation to preserve the diversity of the sgRNA library.
“To preserve the diversity of the library, at least 2000-fold colonies per sgRNA clone were recovered in each transformation.”
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 givenReads were mapped allowing 1 mismatch, and sequences that mapped to more than 1 single site were discarded.
“We allowed 1 mismatch, and discarded any sequences that mapped to more than 1 single site.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenAny preps with cross contamination larger than 1% of the total mappable reads were excluded.
“We excluded any preps with cross contamination larger than 1% of the total mappable reads.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).
InterpretationreasoningIt is likely that HBO1 and ZMYND8 will play important roles in other facets of liver biology and disease.
“Considering the multiple roles that YAP plays in the liver, it is likely that HBO1 and ZMYND8 will play important roles in other facets of liver biology and disease.”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim. May combine two claims.
Study design and conductown dataThe dose of plasmids delivered was titrated to achieve an average integration frequency of one transposon per cell, thereby resulting in a single gene knockout per hepatocyte.
“Moreover, the dose of plasmids delivered was titrated to achieve an average integration frequency of one transposon per cell, thereby resulting in a single gene knockout per hepatocyte (Figure S2C).”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenEach transcription factor or histone factor was normalized separately from the others.
“Each TF or histone factor was normalized separately from others.”
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 givenFor statistical analysis of image quantification results, each lane represents a different biological replicate, and each dot within the lanes indicates measurement values from technical replicates.
“For statistical analysis of image quantification results, each lane represents a different biological replicate, while each dot within the lanes indicates measurement values from technical replicates.”
Quote in the paperNot a substantial claimMay combine two claims.
Study design and conductown dataThere was little to no change in the representation of scramble sgRNAs, whereas sgRNAs targeting the human YAP transgene were collectively the most underrepresented sequences, validating the screening approach.
“As expected, there was little to no change in the representation of scramble sgRNAs, whereas sgRNAs targeting the human YAP transgene were, collectively, the most underrepresented sequences, validating our screening approach (Figure 2F and 2G).”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenFor comparing scATAC and bulk ATAC datasets, peaks defined by scATAC data were used.
“For comparing scATAC and bulk ATAC datasets, peaks defined by scATAC data were used.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Interpretationown dataOur data suggest that much larger and complex libraries (up to 10-fold) could be screened.
“Although our experiments described here utilize an intermediate size library, our data suggest that much larger and complex libraries (up to 10-fold) could be screened.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataInter-sample contamination was assessed and excluded by measuring sgRNA reads corresponding to distinct sgRNA pools within the same sequencing sample.
“As an additional quality control, inter-sample contamination was assessed and excluded by measuring sgRNA reads corresponding to distinct sgRNA pools within the same sequencing sample.”
Quote in the paperNot a substantial claim
The paper relies on this without support.
A major gap exists in knowledge of the nature of the epigenetic changes that occur during hepatocyte reprogramming.
“However, a major gap in our knowledge is the nature of the epigenetic changes that occur during this reprogramming journey.”
The paper relies on this without support.
The identity of epigenetic regulators underlying the hepatocyte-to-BEC cell fate transition is elusive.
“Additionally, the identity of epigenetic regulators underlying this cell fate transition is elusive.”
The paper relies on this without support.
EPCAM is a late stage biliary reprogramming marker.
“We isolated hepatocyte-derived reprogrammed cells through EPCAM (a late stage biliary reprogramming marker) and TOM expression (Figure S1A)”
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.
DDC is given two different chemical names
MinorThe same DDC treatment is identified as dihydrocollidine in the Results and dihydroxychollidine in the Methods. These are different chemical names, so the identity of the administered compound is inconsistent.
“3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)”
“3,5-diethoxycarbonyl-1,4-dihydroxychollidine (DDC)”
Newly generated plasmid conflicts with materials-availability statement
MinorThe materials-availability statement says the study generated no new unique reagents, but the methods explicitly say the authors cloned SB100 into a vector to generate an AAV-virus expression plasmid.
“This study did not generate new unique reagents.”
“SB100 cDNA was cloned into the pTBG AAV-virus vector to generate a SB100 AAV-virus expression plasmid.”
Cites
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works
Comprehensive Integration of Single-Cell Data
Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell · doi:10.1016/j.cell.2019.05.031 · Cited by 15,453 · see citing works
Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1754 · Cited by 15,390 · see citing works
Mootha, V. K., Lindgren, C. M., Eriksson, K.-F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstråle, M., Laurila, E., et al. (2003) · Nature Genetics · doi:10.1038/ng1180 · Cited by 10,197 · see citing works
Statistical significance for genomewide studies
Storey, J. D., & Tibshirani, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1530509100 · Cited by 9,692 · see citing works
deepTools2: a next generation web server for deep-sequencing data analysis
Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., Heyne, S., Dündar, F., & Manke, T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw257 · Cited by 8,096 · see citing works
deepTools: a flexible platform for exploring deep-sequencing data
Ramírez, F., Dündar, F., Diehl, S., Grüning, B. A., & Manke, T. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku365 · Cited by 3,738 · see citing works
An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues
Corces, M. R., Trevino, A. E., Hamilton, E. G., Greenside, P. G., Sinnott-Armstrong, N. A., Vesuna, S., Satpathy, A. T., Rubin, A. J., Montine, K. S., Wu, B., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4396 · Cited by 2,496 · see citing works
Single-cell chromatin accessibility reveals principles of regulatory variation
Buenrostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., Chang, H. Y., & Greenleaf, W. J. (2015) · Nature · doi:10.1038/nature14590 · Cited by 2,308 · see citing works
Self-citationHippo pathway in organ size control, tissue homeostasis, and cancer
Yu, F.-X., Zhao, B., & Guan, K.-L. (2015) · Cell · doi:10.1016/j.cell.2015.10.044 · Cited by 2,206 · see citing works
Smith, T. S., Heger, A., & Sudbery, I. M. (2017) · Genome Research · doi:10.1101/gr.209601.116 · Cited by 2,072 · see citing works
CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling
Platt, R. J., Chen, S., Zhou, Y., Yim, M. J., Swiech, L., Kempton, H. R., Dahlman, J. E., Parnas, O., Eisenhaure, T. M., Jovanovic, M., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.014 · Cited by 2,001 · see citing works
Hydrodynamics-based transfection in animals by systemic administration of plasmid DNA
Liu, F., Song, Y. K., & Liu, D. (1999) · Gene Therapy · doi:10.1038/sj.gt.3300947 · Cited by 1,728 · see citing works
chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
Schep, A. N., Wu, B., Buenrostro, J. D., & Greenleaf, W. J. (2017) · Nature Methods · doi:10.1038/nmeth.4401 · Cited by 1,680 · see citing works
Self-citationYAP1 increases organ size and expands undifferentiated progenitor cells
Camargo, F. D., Gokhale, S., Johnnidis, J. B., Fu, D., Bell, G. W., Jaenisch, R., & Brummelkamp, T. R. (2007) · Current Biology · doi:10.1016/j.cub.2007.10.039 · Cited by 1,252 · see citing works
Self-citationMultiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
Cusanovich, D. A., Daza, R., Adey, A., Pliner, H. A., Christiansen, L., Gunderson, K. L., Steemers, F. J., Trapnell, C., & Shendure, J. (2015) · Science · doi:10.1126/science.aab1601 · Cited by 1,248 · see citing works
Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth
Zanconato, F., Forcato, M., Battilana, G., Azzolin, L., Quaranta, E., Bodega, B., Rosato, A., Bicciato, S., Cordenonsi, M., & Piccolo, S. (2015) · Nature Cell Biology · doi:10.1038/ncb3216 · Cited by 1,219 · see citing works
Hippo–YAP/TAZ signalling in organ regeneration and regenerative medicine
Moya, I. M., & Halder, G. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0086-y · Cited by 981 · see citing works
Hippo Pathway Activity Influences Liver Cell Fate
Yimlamai, D., Christodoulou, C., Galli, G. G., Yanger, K., Pepe-Mooney, B., Gurung, B., Shrestha, K., Cahan, P., Stanger, B. Z., & Camargo, F. D. (2014) · Cell · doi:10.1016/j.cell.2014.03.060 · Cited by 857 · see citing works
Self-citationZhang, N., Bai, H., David, K. K., Dong, J., Zheng, Y., Cai, J., Giovannini, M., Liu, P., Anders, R. A., & Pan, D. (2010) · Developmental Cell · doi:10.1016/j.devcel.2010.06.015 · Cited by 804 · see citing works
CRISPR-mediated direct mutation of cancer genes in the mouse liver
Xue, W., Chen, S., Yin, H., Tammela, T., Papagiannakopoulos, T., Joshi, N. S., Cai, W., Yang, G., Bronson, R., Crowley, D. G., et al. (2014) · Nature · doi:10.1038/nature13589 · Cited by 776 · see citing works
Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains
Shi, J., Wang, E., Milazzo, J. P., Wang, Z., Kinney, J. B., & Vakoc, C. R. (2015) · Nature Biotechnology · doi:10.1038/nbt.3235 · Cited by 739 · see citing works
Dedifferentiation, transdifferentiation and reprogramming: three routes to regeneration
Jopling, C., Boué, S., & Belmonte, J. C. I. (2011) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3043 · Cited by 724 · see citing works
The Hippo pathway effectors TAZ and YAP in development, homeostasis and disease
Varelas, X. (2014) · Development · doi:10.1242/dev.102376 · Cited by 665 · see citing works
Doyon, Y., Cayrou, C., Ullah, M., Landry, A.-J., Côté, V., Selleck, W., Lane, W. S., Tan, S., Yang, X., & Côté, J. (2006) · Molecular Cell · doi:10.1016/j.molcel.2005.12.007 · Cited by 656 · see citing works
Wu, S., Liu, Y., Zheng, Y., Dong, J., & Pan, D. (2008) · Developmental Cell · doi:10.1016/j.devcel.2008.01.007 · Cited by 640 · see citing works
The TEAD/TEF family of transcription factor Scalloped mediates Hippo signaling in organ size control
Zhang, L., Ren, F., Zhang, Q., Chen, Y., Wang, B., & Jiang, J. (2008) · Developmental Cell · doi:10.1016/j.devcel.2008.01.006 · Cited by 630 · see citing works
Bipotential Adult Liver Progenitors Are Derived from Chronically Injured Mature Hepatocytes
Tarlow, B. D., Pelz, C., Naugler, W. E., Wakefield, L., Wilson, E. M., Finegold, M. J., & Grompe, M. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.09.008 · Cited by 533 · see citing works
Robust cellular reprogramming occurs spontaneously during liver regeneration
Yanger, K., Zong, Y., Maggs, L. R., Shapira, S. N., Maddipati, R., Aiello, N. M., Thung, S. N., Wells, R. G., Greenbaum, L. E., & Stanger, B. Z. (2013) · Genes & Development · doi:10.1101/gad.207803.112 · Cited by 484 · see citing works
cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data
Bravo González-Blas, C., Minnoye, L., Papasokrati, D., Aibar, S., Hulselmans, G., Christiaens, V., Davie, K., Wouters, J., & Aerts, S. (2019) · Nature Methods · doi:10.1038/s41592-019-0367-1 · Cited by 456 · see citing works
Adult Hepatocytes Are Generated by Self-Duplication Rather than Stem Cell Differentiation
Yanger, K., Knigin, D., Zong, Y., Maggs, L., Gu, G., Akiyama, H., Pikarsky, E., & Stanger, B. Z. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.06.003 · Cited by 426 · see citing works
YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers
Stein, C., Bardet, A. F., Roma, G., Bergling, S., Clay, I., Ruchti, A., Agarinis, C., Schmelzle, T., Bouwmeester, T., Schübeler, D., et al. (2015) · PLOS Genetics · doi:10.1371/journal.pgen.1005465 · Cited by 414 · see citing works
Klaunig, J. E., Goldblatt, P. J., Hinton, D. E., Lipsky, M. M., Chacko, J., & Trump, B. F. (1981) · In Vitro Cellular & Developmental Biology - Plant · doi:10.1007/bf02618288 · Cited by 404 · see citing works
Cholangiocyte organoids can repair bile ducts after transplantation in the human liver
Sampaziotis, F., Muraro, D., Tysoe, O. C., Sawiak, S., Beach, T. E., Godfrey, E. M., Upponi, S. S., Brevini, T., Wesley, B. T., Garcia-Bernardo, J., et al. (2021) · Science · doi:10.1126/science.aaz6964 · Cited by 394 · see citing works
Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development
Nord, A. S., Blow, M. J., Attanasio, C., Akiyama, J. A., Holt, A., Hosseini, R., Phouanenavong, S., Plajzer-Frick, I., Shoukry, M., Afzal, V., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.033 · Cited by 375 · see citing works
The MYST family of histone acetyltransferases and their intimate links to cancer
Avvakumov, N., & Côté, J. (2007) · Oncogene · doi:10.1038/sj.onc.1210608 · Cited by 356 · see citing works
Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes
Stergachis, A. B., Neph, S. J., Reynolds, A. P., Humbert, R., Miller, B. G., Paige, S. L., Vernot, B., Cheng, J. B., Thurman, R. E., Sandstrom, R. S., et al. (2013) · Cell · doi:10.1016/j.cell.2013.07.020 · Cited by 331 · see citing works
Michalopoulos, G. K., Barua, L., & Bowen, W. C. (2005) · Hepatology · doi:10.1002/hep.20600 · Cited by 319 · see citing works
YAP Drives Growth by Controlling Transcriptional Pause Release from Dynamic Enhancers
Galli, G. G., Carrara, M., Yuan, W.-C., Valdes-Quezada, C., Gurung, B., Pepe-Mooney, B., Zhang, T., Geeven, G., Gray, N. S., de Laat, W., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.09.001 · Cited by 290 · see citing works
Self-citationDe novo formation of the biliary system by TGFβ-mediated hepatocyte transdifferentiation
Schaub, J. R., Huppert, K. A., Kurial, S. N. T., Hsu, B. Y., Cast, A. E., Donnelly, B., Karns, R. A., Chen, F., Rezvani, M., Luu, H. Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0075-5 · Cited by 289 · see citing works
YAP Partially Reprograms Chromatin Accessibility to Directly Induce Adult Cardiogenesis In Vivo
Monroe, T. O., Hill, M. C., Morikawa, Y., Leach, J. P., Heallen, T., Cao, S., Krijger, P. H. L., de Laat, W., Wehrens, X. H. T., Rodney, G. G., et al. (2019) · Developmental Cell · doi:10.1016/j.devcel.2019.01.017 · Cited by 289 · see citing works
Jadhav, U., Saxena, M., O’Neill, N. K., Saadatpour, A., Yuan, G., Herbert, Z. T., Murata, K., & Shivdasani, R. A. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.05.001 · Cited by 283 · see citing works
Pepe-Mooney, B. J., Dill, M. T., Alemany, A., Ordovas-Montanes, J., Matsushita, Y., Rao, A., Sen, A., Miyazaki, M., Anakk, S., Dawson, P. A., et al. (2019) · Cell Stem Cell · doi:10.1016/j.stem.2019.04.004 · Cited by 266 · see citing works
Self-citationBroadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity
Kim, T.-H., Li, F., Ferreiro-Neira, I., Ho, L.-L., Luyten, A., Nalapareddy, K., Long, H., Verzi, M., & Shivdasani, R. A. (2014) · Nature · doi:10.1038/nature12903 · Cited by 257 · see citing works
Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma
LaFave, L. M., Kartha, V. K., Ma, S., Meli, K., Priore, I. S. D., Lareau, C. A., Naranjo, S., Westcott, P. M. K., Duarte, F. M., Sankar, V., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.06.006 · Cited by 207 · see citing works
Self-citationGene regulatory programmes of tissue regeneration
Goldman, J. A., & Poss, K. D. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0239-7 · Cited by 200 · see citing works
Mishima, Y., Miyagi, S., Saraya, A., Negishi, M., Endoh, M., Endo, T. A., Toyoda, T., Shinga, J., Katsumoto, T., Chiba, T., et al. (2011) · Blood · doi:10.1182/blood-2011-01-331892 · Cited by 199 · see citing works
Lee, D.-H., Park, J. O., Kim, T.-S., Kim, S.-K., Kim, T.-H., Kim, M.-C., Park, G. S., Kim, J.-H., Kuninaka, S., Olson, E. N., et al. (2016) · Nature Communications · doi:10.1038/ncomms11961 · Cited by 196 · see citing works
Kastan, N. R., Gnedeva, K., Alisch, T., Petelski, A. A., Huggins, D. J., Chiaravalli, J., Aharanov, A., Shakked, A., Tzahor, E., Nagiel, A., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23395-3 · Cited by 188 · see citing works
Suppression of Enhancer Overactivation by a RACK7-Histone Demethylase Complex
Shen, H., Xu, W., Guo, R., Rong, B., Gu, L., Wang, Z., He, C., Zheng, L., Hu, X., Hu, Z., et al. (2016) · Cell · doi:10.1016/j.cell.2016.02.064 · Cited by 184 · see citing works
Exchange of associated factors directs a switch in HBO1 acetyltransferase histone tail specificityPreprint
Lalonde, M., Avvakumov, N., Glass, K. C., Joncas, F., Saksouk, N., Holliday, M., Paquet, É. R., Yan, K., Tong, Q., Klein, B. J., et al. (2013) · Genes & Development · doi:10.1101/gad.223396.113 · Cited by 181 · see citing works
Cell Plasticity in Liver Regeneration
Li, W., Li, L., & Hui, L. (2020) · Trends in Cell Biology · doi:10.1016/j.tcb.2020.01.007 · Cited by 167 · see citing works
Epigenetic remodelling licences adult cholangiocytes for organoid formation and liver regeneration
Aloia, L., McKie, M. A., Vernaz, G., Cordero-Espinoza, L., Aleksieva, N., van den Ameele, J., Antonica, F., Font-Cunill, B., Raven, A., Aiese Cigliano, R., et al. (2019) · Nature Cell Biology · doi:10.1038/s41556-019-0402-6 · Cited by 160 · see citing works
HBO1 is required for the maintenance of leukaemia stem cells
MacPherson, L., Anokye, J., Yeung, M. M., Lam, E., Chan, Y.-C., Weng, C., Yeh, P., Knezevic, K., Butler, M. S., Hoegl, A., et al. (2019) · Nature · doi:10.1038/s41586-019-1835-6 · Cited by 158 · see citing works
Epithelial Plasticity during Liver Injury and Regeneration
Gadd, V. L., Aleksieva, N., & Forbes, S. J. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2020.08.016 · Cited by 142 · see citing works
Li, N., Li, Y., Lv, J., Zheng, X., Wen, H., Shen, H., Zhu, G., Chen, T.-Y., Dhar, S. S., Kan, P.-Y., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.06.035 · Cited by 141 · see citing works
CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis
Zhu, Q., Liu, N., Orkin, S. H., & Yuan, G. (2019) · Genome biology · doi:10.1186/s13059-019-1802-4 · Cited by 134 · see citing works
Self-citationChromatin plasticity and genome organization in pluripotent embryonic stem cells
Mattout, A., & Meshorer, E. (2010) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2010.02.001 · Cited by 130 · see citing works
Targeting IRF3 as a YAP agonist therapy against gastric cancer
Jiao, S., Guan, J., Chen, M., Wang, W., Li, C., Wang, Y., Cheng, Y., & Zhou, Z. (2018) · The Journal of Experimental Medicine · doi:10.1084/jem.20171116 · Cited by 114 · see citing works
Limaye, P. B., Alarcón, G., Walls, A. L., Nalesnik, M. A., Michalopoulos, G. K., Demetris, A. J., & Ochoa, E. R. (2008) · Laboratory Investigation · doi:10.1038/labinvest.2008.56 · Cited by 94 · see citing works
YAP-dependent proliferation by a small molecule targeting annexin A2
Shalhout, S. Z., Yang, P., Grzelak, E. M., Nutsch, K., Shao, S., Zambaldo, C., Iaconelli, J., Ibrahim, L. H., Stanton, C. R., Chadwick, S. R., et al. (2021) · Nature Chemical Biology · doi:10.1038/s41589-021-00755-0 · Cited by 82 · see citing works
Self-citationYorkie Promotes Transcription by Recruiting a Histone Methyltransferase Complex
Oh, H., Slattery, M. G., Ma, L., White, K. P., Mann, R. S., & Irvine, K. D. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.06.017 · Cited by 77 · see citing works
Jin, H., Kasper, L. H., Larson, J. D., Wu, G., Baker, S. J., Zhang, J., & Fan, Y. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btz720 · Cited by 57 · see citing works
Bell, J. B., Aronovich, E. L., Schreifels, J. M., Beadnell, T. C., & Hackett, P. B. (2010) · Molecular Therapy · doi:10.1038/mt.2010.152 · Cited by 45 · see citing works
Dynamic Transcriptional and Epigenetic Changes Drive Cellular Plasticity in the Liver
Merrell, A. J., Peng, T., Li, J., Sun, K., Li, B., Katsuda, T., Grompe, M., Tan, K., & Stanger, B. Z. (2021) · Hepatology · doi:10.1002/hep.31704 · Cited by 42 · see citing works
Double duty: ZMYND8 in the DNA damage response and cancer
Gong, F., & Miller, K. M. (2018) · Cell Cycle · doi:10.1080/15384101.2017.1376150 · Cited by 36 · see citing works
Cellular reprogramming in vivo initiated by SOX4 pioneer factor activity
Katsuda, T., Sussman, J. H., Ito, K., Katznelson, A., Yuan, S., Takenaka, N., Li, J., Merrell, A. J., Cure, H., Li, Q., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-45939-z · Cited by 33 · see citing works
Kwon, S.-B., Park, J.-S., Yi, J.-Y., et al. (2008) · Toxicologic Pathology · doi:10.1177/0192623308320272 · Cited by 19 · see citing works
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Transcription regulation of cell fate plasticity — from embryonic development to tissue regeneration
Zhao, W., Huang, X., & Xu, C. (2026) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2026.102507 · Cited by 2 · see citing works
Transitional cell states at the crossroads of development, disease, and repair-regeneration
Ke, X., & Cardoso, W. V. (2026) · Physiological Reviews · doi:10.1152/physrev.00041.2025 · Cited by 1 · see citing works
HBO1 promotes replication stress response through ATR-dependent phosphorylation of Ser50/53Preprint
Shen, J., Zong, C., Zhang, Z., Wang, Y., Fang, Y., Zheng, G., & Li, Q. (2025) · Research Square · doi:10.21203/rs.3.rs-6875450/v1
Chen, Y., Zeng, F., Liao, S., et al. (2026) · Cancer Immunology Immunotherapy · doi:10.1007/s00262-026-04491-z
Shen, J., Zhang, J., Zhang, Z., Cai, Y., Wang, Y., Fang, Y., Zheng, G., Li, Q., Wang, L., & Shen, J. (2026) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2026.113419
Chenhao, J., Lu, H., Liu, Y., Jianhao, Z., Chen, H., Xinyun, W., Chi, X., Fan, L., Li, T., Shi, S., et al. (2026) · Journal of Hepatology · doi:10.1016/j.jhep.2026.08.036
Self-citationLee, V., Chiang, C., Balogun, O., Cornuet, P. K., Carson, M., Aggarwal, R., Case, R., IV, Goel, C., El-Mossier, S. O., Liu, J.-J., et al. (2026) · American Journal Of Pathology · doi:10.1016/j.ajpath.2026.09.003
- Authors
- Yuan, W.-C., Earl, A. S., Ma, S., Alcedo, K., Russell, J. O., Duarte, F. M., Chu, Y.-T., Chang, P.-C., Chen, H.-Y., Chi, H.-H., Zhu, Q., Rodriguez-Fraticelli, A. E., Patel, S. H., Lee, Y.-R., Buenrostro, J. D., & Camargo, F. D.
- Affiliations
- Boston Children's Hospital (US)
- Broad Institute (US)
- National Yang Ming Chiao Tung University (TW)
- Institute of Biomedical Sciences, Academia Sinica (TW)
- Harvard University (US)
- Corresponding author
- Yuan, Wei-Chien
- Camargo, Fernando D.
- ORCID
- Venue
- Cell Stem Cell
- Publisher
- Elsevier BV
- Published
- 2025-06
- Volume
- 32
- Issue
- 6
- Pages
- 990-1005.e8
- ISSN
- 1875-9777 (ISSN-L)
- 1934-5909
- PMC
- PMC12598758
- OpenAlex
- W4410550728
- Semantic Scholar
- 3930904f10d7e9f809c7a26103328a26b8d0a10a
- Cited by
- 7
- References
- 72
- Citations by year
- 2026: 6 · 2025: 1
- FWCI
- 3.36
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (am, 369 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell stem cell (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion)
- Funders
- Academia Sinica (110-2320-B-001-029-MY2, 112-2628-B-001-010-MY3, AS-CDA-110-L07)
- National Science and Technology Council (112-2628-B-A49-006, 111-2628-B-A49-019, 110-2628-B-A49A-515, 113-2311-B-A49-006-MY3, 113-2628-B-A49-006)
- National Health Research Institutes (NHRI-EX114-11415BC)
- National Institutes of Health (AR064036, DK099559, P30DK034854)
- Harvard Digestive Diseases Center, Harvard University
- National Yang Ming Chiao Tung University
- National Cancer Center (AS-CFII112-204)
- Ministry of Education (MOE-108-YSFMS-0004-012-P1, 112W31101, 113W031101, 114W031101)
- Topics
- Health Sciences › Medicine › Hepatology › Liver physiology and pathology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Hippo pathway signaling and YAP/TAZ
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- HBO1, liver injury, chromatin remodeling, H3K14 acetylation, ZMYND8, histone acetyltransferase, epigenetic regulation, liver regeneration, chromatin dynamics
- MeSH terms
- Cell Plasticity, YAP-Signaling Proteins, Acetylation, Animals, Histones, Humans, Liver, Liver Regeneration, Transcription Factors, Hepatocytes, Chromatin Assembly and Disassembly, Epigenesis, Genetic, Adaptor Proteins, Signal Transducing, Mice, Histone Acetyltransferases, Cellular Reprogramming
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-22.
Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-22.
Cited sources are checked by gpt-6-sol.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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