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PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression.
Open accessAbstract
While reversible histone modifications are linked to an ever-expanding range of biological functions, the demethylases for histone H4 lysine 20 and their potential regulatory roles remain unknown. Here we report that the PHD and Jumonji C (JmjC) domain-containing protein, PHF8, while using multiple substrates, including H3K9me1/2 and H3K27me2, also functions as an H4K20me1 demethylase. PHF8 is recruited to promoters by its PHD domain based on interaction with H3K4me2/3 and controls G1-S transition in conjunction with E2F1, HCF-1 (also known as HCFC1) and SET1A (also known as SETD1A), at least in part, by removing the repressive H4K20me1 mark from a subset of E2F1-regulated gene promoters. Phosphorylation-dependent PHF8 dismissal from chromatin in prophase is apparently required for the accumulation of H4K20me1 during early mitosis, which might represent a component of the condensin II loading process. Accordingly, the HEAT repeat clusters in two non-structural maintenance of chromosomes (SMC) condensin II subunits, N-CAPD3 and N-CAPG2 (also known as NCAPD3 and NCAPG2, respectively), are capable of recognizing H4K20me1, and ChIP-Seq analysis demonstrates a significant overlap of condensin II and H4K20me1 sites in mitotic HeLa cells. Thus, the identification and characterization of an H4K20me1 demethylase, PHF8, has revealed an intimate link between this enzyme and two distinct events in cell cycle progression.
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“As we discussed in the Cell Cycle Regulation section, USP7 deubiquitinates and stabilizes PHF8, allowing the latter to upregulate gene targets involved in cell cycle progression, including cyclin A2 (Liu et al., 2010; Wang et al., 2016).”
From USP7 Is a Master Regulator of Genome Stability (2020) · cites this paper as Liu et al., 2010
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“It is well established for other histone Lys demethylases, such as PHF8, KDM7A, and KDM4, that they have dual specificity depending on the chromatin context and the presence of other binding factors (Klose et al., 2006b; Horton et al., 2010; Lin et al., 2010; Liu et al., 2010b; Yang et al., 2010).”
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“In addition the activity of histone modifiers can be regulated in a cell cycledependent manner [9-14].”
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“…soon after ORI activation, Set7 is degraded by the proteasome in a PCNA (PROLIFERATING CELL NUCLEAR ANTIGEN)- and Cul (CULLIN)-Ddb1 (DNA DAMAGE BINDING PROTEIN 1)-dependent manner and, as a consequence, the levels of H4K20me1 fall sharply (Oda et al., 2009; Liu et al., 2010; Tardat et al., 2010).”
BackgroundJMJD-1.2/PHF8 controls axon guidance by regulating Hedgehog-like signaling
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“While the JmjC domain of PHF8 catalyzes the removal of H3K9me2/me1 and H4K20me1, its PHD finger binds H3K4me3 and contributes to the demethylase activity of the protein at appropriate target sites (Feng et al., 2010; Kleine-Kohlbrecher et al., 2010; Liu et al., 2010).”
BackgroundSpatial Proximity and Similarity of the Epigenetic State of Genome Domains
Khrameeva, E. E., Mironov, A. A., Fedonin, G. G., Khaitovich, P., & Gelfand, M. S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033947 · Cited by 20
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“Consistent with this, hCAPD3 and hCAPG2 are reported to interact with H4K20me1 histone tails and support specific association between H4K20me1 and condensin II [72].”
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Self-citationCK2 kinase-mediated PHF8 phosphorylation controls TopBP1 stability to regulate DNA replication
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Self-citationTargeting the PHF8/YY1 axis suppresses cancer cell growth through modulation of ROS
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“S8 S and T ), which supports the specificity of iPHF8. iPHF8 treatment led to a significant increase of cellular H3K9me1/2 and H4K20me1 levels, but not H3K4me2, H3K36me3, and H3K79me2 levels (Fig.”
BackgroundSelf-citationHistone demethylase PHF8 regulates hypoxia signaling through HIF1α and H3K4me3
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“PHF8 has been reported to interact with components of the H3K4me3 methyltransferase complex, including SETA1 [30] and WDR5 [31], and PHF8 knockdown impairs the recruitment of SETA1 [30].”
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The TFIIH complex is required to establish and maintain mitotic chromosome structure
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“As the identified transcription factors are known chromatin binders [69 – 75], we also included histone marks in the analysis.”
STAG2 Regulates Homologous Recombination Repair and Sensitivity to ATM Inhibition
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“Human condensin II binds monomethylated H4-K20 and tends to colocalize with this mark on chromosomes (Liu et al. 2010).”
The histone demethylase PHF8 is a molecular safeguard of the IFNγ response
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“PHF8 is the only HDM responsible for demethylating H4K20me1 (17,18).”
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“An aliquot of cDNA was generated from 1–2 g of total RNA using the TaqMan Reverse Transcription Reagents (Applied Biosystems) and an oligo-dT(16) primer (Invitrogen).”
MethodCondensins and 3D Organization of the Interphase Nucleus
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“raising the possibility that the DCC might bind directly to H4K20me1 to affect compaction of chromatin [92].”
BackgroundPHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression
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“Moreover, condensin can recognize and bind monomethylated H4K20, inducing compaction, while dimethylated H4K20 disrupts condensin association to DNA, and consequently leads to decondensation [145].”
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“…and H3K27me2/1 (Horton et al. 2010; Huang et al. 2010b; Tsukada et al. 2010); PHF8, which demethylates H3K9me2/me1 and H4K20me1 (Horton et al. 2010; Liu et al. 2010; Loenarz et al. 2010; Qi et al. 2010); and PHF2, which targets H3K9me2/me1 and H4K20me3 (Wen et al. 2010; Baba et al. 2011; Stender…”
The histone H4 lysine 20 demethylase DPY-21 regulates the dynamics of condensin DC binding
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“While PHF8 was recently identified as having H4K20me1 demethylase activity and is involved in cell cycle progression, its role, if any, in regulating DDRspecific H4K20 methylation is unknown (Liu et al. 2010).”
BackgroundFan, T., Xie, J., Huang, G. C., Li, L., Zeng, X., & Tao, Q. (2024) · Epigenomes · doi:10.3390/epigenomes8030036 · Cited by 13
“…localized at the transcription start site (TSS) and acts on the following histone lysine sites: H3K9me1/2, H3K27me2, H4K20me1, and H3K36me2 [35,41], which upon the initiation of PHF8 demethylase activity cause varying degrees of histone demethylation and lead to PHF8-associated…”
BackgroundHistone Methylation in Myelodysplastic Syndromes
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Histone modification profiles characterize function-specific gene regulation
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“condensin II have utilized cell lines that are transformed by viral oncogenes that target RB (13, 42).”
BackgroundComparative distributions of RSBN1 and methylated histone H4 Lysine 20 in the mouse spermatogenesis
Wang, Y., Iwamori, T., Kaneko, T., Iida, H., & Iwamori, N. (2021) · PLoS ONE · doi:10.1371/journal.pone.0253897 · Cited by 13
Development of Substrate-Selective Probes for Affinity Pulldown of Histone Demethylases
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The histone demethylase PHF8 regulates astrocyte differentiation and function
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SMYD5 acts as a potential biomarker for hepatocellular carcinoma
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Current advances and future directions in targeting histone demethylases for cancer therapy
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The chemistry and biology of the α-ketoglutarate-dependent histone N ε -methyl-lysine demethylases
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Determinants of Human Cyclin B1 Association with Mitotic Chromosomes
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“lated histone H4K20 that promotes condensin binding [19].”
BackgroundArtificial generation of centromeres and kinetochores to understand their structure and function
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Dynamic Control of Chromosome Topology and Gene Expression by a Chromatin ModificationPreprint
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“[PubMed: 21363964] Qi HH, Sarkissian M, Hu GQ, Wang Z, Bhattacharjee A, Gordon DB, Gonzales M, Lan F, Ongusaha PP, Huarte M, et al. Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development.”
InfluentialLi, W., Chen, Y.-C., Lin, Y., Zou, Y.-Q., Hu, G.-S., Yang, J.-J., Nie, X. Y., Li, M.-Y., Wang, Y., He, Y., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115487 · Cited by 12
Self-citationRegulatory mechanism of androgen receptor on NCAPD3 gene expression in prostate cancer
Yin, Y., Liu, Q., Shao, Y., He, X., Zhu, Q., Lu, S., & Liu, P. (2021) · The Prostate · doi:10.1002/pros.24245 · Cited by 10
Chromatin dynamics from S-phase to mitosis: contributions of histone modifications
Doenecke, D. (2014) · Cell and Tissue Research · doi:10.1007/s00441-014-1873-1 · Cited by 10
Dorosz, J., Olsen, L., Seger, S. T., Steinhauer, C., Bouras, G., Helgstrand, C., Wiuf, A., & Gajhede, M. (2017) · ChemBioChem · doi:10.1002/cbic.201700109 · Cited by 10
Downregulation of lncRNA FGF12-AS2 suppresses the tumorigenesis of NSCLC via sponging miR-188-3p
Zhou, L., Chen, X., Zhou, D., Yang, R., & Cai, M. (2020) · Open Medicine · doi:10.1515/med-2020-0219 · Cited by 10
Benefits and pitfalls: Epigenetic modulators in prostate cancer intervention
Upadhyay, N., Tilekar, K. N., Hess, J. D., Pokrovsky, V. S., Aguilera, R. J., & Ramaa, C. S. (2021) · Current Research in Chemical Biology · doi:10.1016/j.crchbi.2021.100006 · Cited by 11
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The Molecular Basis of Histone Demethylation
Horton, J. R., Gale, M., Yan, Q., & Cheng, X. (2017) · Cancer drug discovery and develogment/Cancer drug discovery and development · doi:10.1007/978-3-319-59786-7_7 · Cited by 10
The Role of Histone Methylation and Methyltransferases in Gene Regulation
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Taking Me away: the function of phosphorylation on histone lysine demethylases
Karakatsanis, N. M., Hamey, J. J., & Wilkins, M. R. (2024) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2023.12.004 · Cited by 9
Histone Methylation in Chromatin Signaling
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“For example, the TAF3-PHD finger recognizes and binds K4Me3 [55, 56], SIRT6 deacetylates K9ac [57], LSD1 demethylates K9Me2 [58], MKP-1 dephosphorylates S10, and PHF8 demethylates both K9Me1/2 and K27Me2 [59].”
BackgroundIn Vitro Histone Demethylase Assays
Kokura, K., Sun, L., & Fang, J. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-2474-5_8 · Cited by 9
Bookmarking by histone methylation ensures chromosomal integrity during mitosis
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“In addition, phosphorylated PHF8 mediated by CDK1/cyclin B1 during prophase dissociates from chromosomes and allows formation of H4K20me1 at early mitosis (Liu et al. 2010).”
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“…has been implicated in chromatin compaction (Lu et al. 2008) and gene repression (Kalakonda et al. 2008; Abbas et al. 2010; Congdon et al. 2010; Liu et al. 2010) via either its association with the transcriptional repressor L(3)mbt or its localization in inactive regions of the genome…”
Histone lysine methylation modifiers controlled by protein stability
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Disrupting PHF8-TOPBP1 connection elicits a breast tumor-specific vulnerability to chemotherapeutics
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1.4.3 The vector meson nonet (1- states)
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Metadata
- Authors
- Liu, W., Tanasa, B., Tyurina, O. V., Zhou, T. Y., Gassmann, R., Liu, W. T., Ohgi, K. A., Benner, C., Garcia-Bassets, I., Aggarwal, A. K., Desai, A., Dorrestein, P. C., Glass, C. K., & Rosenfeld, M. G.
- Affiliations
- Howard Hughes Medical Institute (US)
- University of California San Diego (US)
- Icahn School of Medicine at Mount Sinai (US)
- Corresponding author
- Rosenfeld, Michael G.
- ORCID
- Venue
- Nature
- Published
- 2010-07
- Volume
- 466
- Issue
- 7305
- Pages
- 508-512
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3059551
- OpenAlex
- W2130239280
- Cited by
- 441
- References
- 43
- Citations by year
- 2026: 10 · 2025: 19 · 2024: 17 · 2023: 39 · 2022: 21 · 2021: 37 · 2020: 16 · 2019: 17 · 2018: 19 · 2017: 35 · 2016: 32 · 2015: 30 · 2014: 33 · 2013: 39 · 2012: 33
- FWCI
- 15.23
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- U.S. Department of Defense
- Howard Hughes Medical Institute
- National Institutes of Health
- University of California, San Diego
- National Heart, Lung, and Blood Institute (R01HL065445)
- National Cancer Institute (R01CA097134)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK039949, R37DK039949, R01DK018477)
- National Institute of Neurological Disorders and Stroke (R01NS034934)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Cancer-related gene regulation
- Keywords
- PHF8, H4K20me1, Jumonji C domain, cell cycle progression, G1/S transition, E2F1, HCF-1, SET1A, X-linked intellectual disability, craniofacial development, neuronal survival, histone demethylase, chromatin regulation, zebrafish, promoter recruitment
- MeSH terms
- Adenosine Triphosphatases, Cell Cycle, Cell Line, Chromatin, Chromosomal Proteins, Non-Histone, DNA-Binding Proteins, HeLa Cells, Histones, Humans, Lysine, Methylation, Phosphorylation, Promoter Regions, Genetic, Histone-Lysine N-Methyltransferase, Transcription Factors, Protein Structure, Tertiary, Multiprotein Complexes, Host Cell Factor C1, Histone Demethylases
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