- Jenuwein, T. & Allis, C.D. Translating the histone code. Science 293, 1074–1080 (2001).
Article CAS Google Scholar
- Felsenfeld, G. & Groudine, M. Controlling the double helix. Nature 421, 448–453 (2003).
Article Google Scholar
- Taverna, S.D., Li, H., Ruthenburg, A.J., Allis, C.D. & Patel, D.J. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 14, 1025–1040 (2007).
Article CAS Google Scholar
- Bird, A.P. & Wolffe, A.P. Methylation-induced repression–belts, braces, and chromatin. Cell 99, 451–454 (1999).
Article CAS Google Scholar
- Jones, P.A. & Baylin, S.B. The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3, 415–428 (2002).
Article CAS Google Scholar
- Freitag, M. & Selker, E.U. Controlling DNA methylation: many roads to one modification. Curr. Opin. Genet. Dev. 15, 191–199 (2005).
Article CAS Google Scholar
- Klose, R.J. & Bird, A.P. Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci. 31, 89–97 (2006).
Article CAS Google Scholar
- Eden, S., Hashimshony, T., Keshet, I., Cedar, H. & Thorne, A.W. DNA methylation models histone acetylation. Nature 394, 842 (1998).
Article CAS Google Scholar
- Schubeler, D. et al. Genomic targeting of methylated DNA: influence of methylation on transcription, replication, chromatin structure, and histone acetylation. Mol. Cell. Biol. 20, 9103–9112 (2000).
Article CAS Google Scholar
- Johnson, L.M. et al. The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr. Biol. 17, 379–384 (2007).
Article CAS Google Scholar
- Fuks, F. et al. The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J. Biol. Chem. 278, 4035–4040 (2003).
Article CAS Google Scholar
- Sarraf, S.A. & Stancheva, I. Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol. Cell 15, 595–605 (2004).
Article CAS Google Scholar
- Tamaru, H. et al. Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat. Genet. 34, 75–79 (2003).
Article CAS Google Scholar
- Fuks, F. DNA methylation and histone modifications: teaming up to silence genes. Curr. Opin. Genet. Dev. 15, 490–495 (2005).
Article CAS Google Scholar
- Schotta, G. et al. A silencing pathway to induce H3–K9 and H4–K20 trimethylation at constitutive heterochromatin. Genes Dev. 18, 1251–1262 (2004).
Article CAS Google Scholar
- Lehnertz, B. et al. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 13, 1192–1200 (2003).
Article CAS Google Scholar
- Fuks, F., Hurd, P.J., Deplus, R. & Kouzarides, T. The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase. Nucleic Acids Res. 31, 2305–2312 (2003).
Article CAS Google Scholar
- Vire, E. et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439, 871–874 (2006).
Article CAS Google Scholar
- van der Ploeg, L.H. & Flavell, R.A. DNA methylation in the human gamma-delta-beta-globin locus in erythroid and non-erythroid cells. Cell 19, 947–958 (1980).
Article CAS Google Scholar
- Zhao, Q. et al. Repression of human gamma-globin gene expression by a short isoform of the NF-E4 protein is associated with loss of NF-E2 and RNA polymerase II recruitment to the promoter. Blood 107, 2138–2145 (2006).
Article CAS Google Scholar
- Pollack, B.P. et al. The human homologue of the yeast proteins Skb1 and Hsl7p interacts with Jak kinases and contains protein methyltransferase activity. J. Biol. Chem. 274, 31531–31542 (1999).
Article CAS Google Scholar
- Huang, S., Litt, M. & Felsenfeld, G. Methylation of histone H4 by arginine methyltransferase PRMT1 is essential in vivo for many subsequent histone modifications. Genes Dev. 19, 1885–1893 (2005).
Article CAS Google Scholar
- Fabbrizio, E. et al. Negative regulation of transcription by the type II arginine methyltransferase PRMT5. EMBO Rep. 3, 641–645 (2002).
Article CAS Google Scholar
- Pal, S., Vishwanath, S.N., Erdjument-Bromage, H., Tempst, P. & Sif, S. Human SWI/SNF-associated PRMT5 methylates histone H3 arginine 8 and negatively regulates expression of ST7 and NM23 tumor suppressor genes. Mol. Cell. Biol. 24, 9630–9645 (2004).
Article CAS Google Scholar
- Branscombe, T.L. et al. PRMT5 (Janus kinase-binding protein 1) catalyzes the formation of symmetric dimethylarginine residues in proteins. J. Biol. Chem. 276, 32971–32976 (2001).
Article CAS Google Scholar
- Goren, A. et al. Fine tuning of globin gene expression by DNA methylation. PLoS ONE 1, e46 (2006).
Article Google Scholar
- Jane, S.M., Ney, P.A., Vanin, E.F., Gumucio, D.L. & Nienhuis, A.W. Identification of a stage selector element in the human gamma-globin gene promoter that fosters preferential interaction with the 5′ HS2 enhancer when in competition with the beta-promoter. EMBO J. 11, 2961–2969 (1992).
Article CAS Google Scholar
- Cheng, X. & Blumenthal, R.M. Mammalian DNA methyltransferases: a structural perspective. Structure 16, 341–350 (2008).
Article Google Scholar
- Maurer-Stroh, S. et al. The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends Biochem. Sci. 28, 69–74 (2003).
Article CAS Google Scholar
- Bienz, M. The PHD finger, a nuclear protein-interaction domain. Trends Biochem. Sci. 31, 35–40 (2006).
Article CAS Google Scholar
- Ooi, S.K. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717 (2007).
Article CAS Google Scholar
- Ancelin, K. et al. Blimp1 associates with Prmt5 and directs histone arginine methylation in mouse germ cells. Nat. Cell Biol. 8, 623–630 (2006).
Article CAS Google Scholar
- Ruthenburg, A.J., Allis, C.D. & Wysocka, J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol. Cell 25, 15–30 (2007).
Article CAS Google Scholar
- Shi, X. et al. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 442, 96–99 (2006).
Article CAS Google Scholar
- Pena, P.V. et al. Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature 442, 100–103 (2006).
Article CAS Google Scholar
- Wysocka, J. et al. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature 442, 86–90 (2006).
Article CAS Google Scholar
- Li, H. et al. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 442, 91–95 (2006).
Article CAS Google Scholar
- Vermeulen, M. et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131, 58–69 (2007).
Article CAS Google Scholar
- Iwase, S. et al. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 128, 1077–1088 (2007).
Article CAS Google Scholar
- Shi, X. et al. Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36. J. Biol. Chem. 282, 2450–2455 (2007).
Article CAS Google Scholar
- Ramon-Maiques, S. et al. The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2. Proc. Natl. Acad. Sci. USA 104, 18993–18998 (2007).
Article CAS Google Scholar
- Cote, J. & Richard, S. Tudor domains bind symmetrical dimethylated arginines. J. Biol. Chem. 280, 28476–28483 (2005).
Article CAS Google Scholar
- Slater, L.M., Allen, M.D. & Bycroft, M. Structural variation in PWWP domains. J. Mol. Biol. 330, 571–576 (2003).
Article CAS Google Scholar
- Fraser, P., Pruzina, S., Antoniou, M. & Grosveld, F. Each hypersensitive site of the human beta-globin locus control region confers a different developmental pattern of expression on the globin genes. Genes Dev. 7, 106–113 (1993).
Article CAS Google Scholar
- Carter, D., Chakalova, L., Osborne, C.S., Dai, Y.F. & Fraser, P. Long-range chromatin regulatory interactions in vivo. Nat. Genet. 32, 623–626 (2002).
Article CAS Google Scholar
- Tolhuis, B., Palstra, R.J., Splinter, E., Grosveld, F. & de Laat, W. Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol. Cell 10, 1453–1465 (2002).
Article CAS Google Scholar
- Demers, C. et al. Activator-mediated recruitment of the MLL2 methyltransferase complex to the beta-globin locus. Mol. Cell 27, 573–584 (2007).
Article CAS Google Scholar
- Saunthararajah, Y. et al. Effects of 5-aza-2′-deoxycytidine on fetal hemoglobin levels, red cell adhesion, and hematopoietic differentiation in patients with sickle cell disease. Blood 102, 3865–3870 (2003).
Article CAS Google Scholar
- Estève, P.O. et al. Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication. Genes Dev. 20, 3089–3103 (2006).
Article Google Scholar
- Smallwood, A., Esteve, P.O., Pradhan, S. & Carey, M. Functional cooperation between HP1 and DNMT1 mediates gene silencing. Genes Dev. 21, 1169–1178 (2007).
Article CAS Google Scholar
- Lindroth, A.M. et al. Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J. 23, 4286–4296 (2004).
Article CAS Google Scholar
- Zhao, Q., Cumming, H., Cerruti, L., Cunningham, J.M. & Jane, S.M. Site-specific acetylation of the fetal globin activator NF-E4 prevents its ubiquitination and regulates its interaction with the histone deacetylase, HDAC1. J. Biol. Chem. 279, 41477–41486 (2004).
Article CAS Google Scholar
- Wysocka, J. et al. WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121, 859–872 (2005).
Article CAS Google Scholar
- Rea, S. et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406, 593–599 (2000).
Article CAS Google Scholar
- Brand, M., Rampalli, S., Chaturvedi, C.P. & Dilworth, F.J. Analysis of epigenetic modifications of chromatin at specific gene loci by native chromatin immunoprecipitation of nucleosomes isolated using hydroxyapatite chromatography. Nat. Protoc. 3, 398–409 (2008).
Article CAS Google Scholar
- Lavelle, D., Vaitkus, K., Hankewych, M., Singh, M. & DeSimone, J. Effect of 5-aza-2′-deoxycytidine (Dacogen) on covalent histone modifications of chromatin associated with the epsilon-, gamma-, and beta-globin promoters in Papio anubis. Exp. Hematol. 34, 339–347 (2006).
Article CAS Google Scholar