Origins and Formation of Histone Methylation across the Human Cell Cycle

REFERENCES

• Abbas T, et al. 2010. CRL4(Cdt2) regulates cell proliferation and histone gene expression by targeting PR-Set7/Set8 for degradation. Mol. Cell 40: 9–21.
   PubMed Web of Science ®Google Scholar
• Aoto T, Saitoh H, Sakamoto Y, Watanabe S, Nakao M. 2008. Polycomb group protein-associated chromatin is reproduced in post-mitotic G1 phase and is required for S phase progression. J. Biol. Chem. 283: 18905–18915.
   PubMedGoogle Scholar
• Araujo FD, Knox JD, Szyf M, Price GB, Zannis-Hadjopoulos M. 1998. Concurrent replication and methylation at mammalian origins of replication. Mol. Cell. Biol. 18: 3475–3482.
   PubMedGoogle Scholar
• Bajad SU, et al. 2006. Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry. J. Chromatogr. A 1125: 76–88.
   PubMed Web of Science ®Google Scholar
• Barski A, et al. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129: 823–827.
   PubMed Web of Science ®Google Scholar
• Bello B, Holbro N, Reichert H. 2007. Polycomb group genes are required for neural stem cell survival in postembryonic neurogenesis of Drosophila. Development 134: 1091–1099.
   PubMedGoogle Scholar
• Bernstein BE, et al. 2006. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315–326.
   PubMed Web of Science ®Google Scholar
• Bracken AP, et al. 2003. EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. EMBO J. 22: 5323–5335.
   PubMed Web of Science ®Google Scholar
• Buchenau P, Hodgson J, Strutt H, Arndt-Jovin DJ. 1998. The distribution of polycomb-group proteins during cell division and development in Drosophila embryos: impact on models for silencing. J. Cell Biol. 141: 469–481.
   PubMed Web of Science ®Google Scholar
• Cao R, et al. 2002. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298: 1039–1043.
   PubMed Web of Science ®Google Scholar
• Carrozza MJ, et al. 2005. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123: 581–592.
   PubMed Web of Science ®Google Scholar
• Cheutin T, et al. 2003. Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science 299: 721–725.
   PubMed Web of Science ®Google Scholar
• Chin HG, Patnaik D, Estève PO, Jacobsen SE, Pradhan S. 2006. Catalytic properties and kinetic mechanism of human recombinant Lys-9 histone H3 methyltransferase SUV39H1: participation of the chromodomain in enzymatic catalysis. Biochemistry 45: 3272–3284.
   PubMedGoogle Scholar
• Deal RB, Henikoff JG, Henikoff S. 2010. Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science 328: 1161–1164.
   PubMed Web of Science ®Google Scholar
• Dion MF, et al. 2007. Dynamics of replication-independent histone turnover in budding yeast. Science 315: 1405–1408.
   PubMed Web of Science ®Google Scholar
• Estève PO, et al. 2006. Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication. Genes Dev. 20: 3089–3103.
   PubMed Web of Science ®Google Scholar
• Graves RA, Pandey NB, Chodchoy N, Marzluff WF. 1987. Translation is required for regulation of histone mRNA degradation. Cell 48: 615–626.
   PubMed Web of Science ®Google Scholar
• Hagstrom K, Schedl P. 1997. Remembrance of things past: maintaining gene expression patterns with altered chromatin. Curr. Opin. Genet. Dev. 7: 814–821.
   PubMedGoogle Scholar
• Heintz N, Sive HL, Roeder RG. 1983. Regulation of human histone gene expression: kinetics of accumulation and changes in the rate of synthesis and in the half-lives of individual histone mRNAs during the HeLa cell cycle. Mol. Cell. Biol. 3: 539–550.
   PubMed Web of Science ®Google Scholar
• Heit R, Rattner JB, Chan GK, Hendzel MJ. 2009. G2 histone methylation is required for the proper segregation of chromosomes. J. Cell Sci. 122: 2957–2968.
   PubMedGoogle Scholar
• Hirota T, Lipp JJ, Toh BH, Peters JM. 2005. Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin. Nature 438: 1176–1180.
   PubMed Web of Science ®Google Scholar
• Holliday R. 1987. The inheritance of epigenetic defects. Science 238: 163–170.
   PubMed Web of Science ®Google Scholar
• Hsu JY, et al. 2000. Mitotic phosphorylation of histone H3 is governed by Ipl1/aurora kinase and Glc7/PP1 phosphatase in budding yeast and nematodes. Cell 102: 279–291.
   PubMed Web of Science ®Google Scholar
• Huen MSY, Sy SMH, van Deursen JM, Chen J. 2008. Direct interaction between SET8 and proliferating cell nuclear antigen couples H4–K20 methylation and DNA replication. J. Biol. Chem. 283: 11073–11077.
   PubMed Web of Science ®Google Scholar
• Jackson V. 1988. Deposition of newly synthesized histones: hybrid nucleosomes are not tandemly arranged on daughter DNA strands. Biochemistry 27: 2109–2120.
   PubMedGoogle Scholar
• Jenuwein T, Allis CD. 2001. Translating the histone code. Science 293: 1074–1080.
   PubMed Web of Science ®Google Scholar
• Jørgensen S, et al. 2007. The histone methyltransferase SET8 is required for S-phase progression. J. Cell Biol. 179: 1337–1345.
   PubMed Web of Science ®Google Scholar
• Julien E, Herr W. 2004. A switch in mitotic histone H4 lysine 20 methylation status is linked to M phase defects upon loss of HCF-1. Mol. Cell 14: 713–725.
   PubMedGoogle Scholar
• Kaneko S, et al. 2010. Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA. Genes Dev. 24: 2615–2620.
   PubMed Web of Science ®Google Scholar
• Kellum R, Raff JW, Alberts BM. 1995. Heterochromatin protein 1 distribution during development and during the cell cycle in Drosophila embryos. J. Cell Sci. 108: 1407–1418.
   PubMedGoogle Scholar
• Kornberg RD, Lorch Y. 1999. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98: 285–294.
   PubMed Web of Science ®Google Scholar
• Krogan NJ, et al. 2003. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol. Cell. Biol. 23: 4207–4217.
   PubMed Web of Science ®Google Scholar
• Liu W, et al. 2010. PHF8 mediates histone H4 lysine 20 demethylation events in cell cycle progression. Nature 466: 508–512.
   PubMed Web of Science ®Google Scholar
• Loyola A, et al. 2009. The HP1α-CAF1-SetDB1-containing complex provides H3K9me1 for Suv39-mediated K9me3 in pericentric heterochromatin. EMBO Rep. 10: 769–775.
   PubMed Web of Science ®Google Scholar
• Martin C, Zhang Y. 2005. The diverse functions of histone lysine methylation. Nat. Rev. Mol. Cell Biol. 6: 838–849.
   PubMed Web of Science ®Google Scholar
• Melcher M, et al. 2000. Structure-function analysis of SUV39H1 reveals a dominant role in heterochromatin organization, chromosome segregation, and mitotic progression. Mol. Cell. Biol. 20: 3728–3741.
   PubMed Web of Science ®Google Scholar
• Ng HH, Robert F, Young RA, Struhl K. 2003. Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol. Cell 11: 709–719.
   PubMed Web of Science ®Google Scholar
• Ong SE, Mittler G, Mann M. 2004. Identifying and quantifying in vivo methylation sites by heavy methyl SILAC. Nat. Methods 1: 119–126.
   PubMed Web of Science ®Google Scholar
• Pesavento JJ, Yang H, Kelleher NL, Mizzen CA. 2008. Certain and progressive methylation of histone H4 and lysine 20 during the cell cycle. Mol. Cell. Biol. 28: 468–486.
   PubMed Web of Science ®Google Scholar
• Prasanth SG, Shen Z, Prasanth KV, Stillman B. 2010. Human origin recognition complex is essential for HP1 binding to chromatin and heterochromatin organization. Proc. Natl. Acad. Sci. U. S. A. 107: 15093–15098.
   PubMed Web of Science ®Google Scholar
• Probst AV, Dunleavy E, Almouzni G. 2009. Epigenetic inheritance during the cell cycle. Nat. Rev. Mol. Cell Biol. 10: 192–206.
   PubMed Web of Science ®Google Scholar
• Rea S, et al. 2000. Regulation of chromatin structure by site-specific histone H3 methyltransferase. Nature 406: 593–599.
   PubMed Web of Science ®Google Scholar
• Rice JC, et al. 2002. Mitotic-specific methylation of histone H4 Lys 20 follows increased PR-Set7 expression and its localization to mitotic chromosomes. Genes Dev. 16: 2225–2230.
   PubMed Web of Science ®Google Scholar
• Sakaguchi A, Karachentsev D, Seth-Pasricha M, Druzhinina M, Steward R. 2008. Functional characterization of the Drosophila Hmt4-20/Suv4-20 histone methyltransferase. Genetics 179: 317–322.
   PubMedGoogle Scholar
• Sarkies P, Sale JE. 2 October 2011. Propagation of histone marks and epigenetic memory during normal and interrupted DNA replication. Cell. Mol. Life Sci. [Epub ahead of print.] https://doi.org/10.1007/s00018-011-0824-1.
   Google Scholar
• Schotta G, et al. 2008. A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse. Genes Dev. 22: 2048–2061.
   PubMed Web of Science ®Google Scholar
• Sittman DB, Graves RA, Marzluff WF. 1983. Histone mRNA concentrations are regulated at the level of transcription and mRNA degradation. Proc. Natl. Acad. Sci. U. S. A. 80: 1849–1853.
   PubMedGoogle Scholar
• Trojer P, et al. 2007. L3MBTL1, a histone-methylation-dependent chromatin lock. Cell 129: 915–928.
   PubMed Web of Science ®Google Scholar
• Wang Z, et al. 2008. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 40: 897–903.
   PubMed Web of Science ®Google Scholar
• Wei Y, Yu L, Bowen J, Gorovsky MA, Allis CD. 1999. Phosphorylation of histone H3 is required for proper chromosome condensation and segregation. Cell 97: 99–109.
   PubMed Web of Science ®Google Scholar
• Xu M, Wang W, Chen S, Zhu B. 4 November 2011. A model for mitotic inheritance of histone lysine methylation. EMBO Rep. [Epub ahead of print.] https://doi.org/10.1038/embor.2011.206.
   Google Scholar
• Xu M, et al. 2010. Partitioning of histone H3–H4 tetramers during DNA replication-dependent chromatin assembly. Science 328: 94–98.
   PubMed Web of Science ®Google Scholar
• Zee BM, et al. 2010. In vivo residue-specific histone methylation dynamics. J. Biol. Chem. 285: 3341–3350.
   PubMed Web of Science ®Google Scholar
• Zee BM, Levin RS, DiMaggio PA, Garcia BA. 2010. Global turnover of histone post-translational modifications and variants in human cells. Epigenetics Chromatin 3: 22.
   PubMed Web of Science ®Google Scholar