High-Resolution Profiling of Histone Methylations in the Human Genome

Abeysinghe, 2004, Gross Rearrangement Breakpoint Database (GRaBD), Hum. Mutat., 23, 219, 10.1002/humu.20006

Allis, 1980, Histone variants specific to the transcriptionally active, amitotically dividing macronucleus of the unicellular eucaryote, Tetrahymena thermophila, Cell, 20, 609, 10.1016/0092-8674(80)90307-4

An, 2004, Ordered cooperative functions of PRMT1, p300 and CARM1 in transcriptional activation by p53, Cell, 117, 735, 10.1016/j.cell.2004.05.009

Bannister, 2005, Spatial distribution of di- and tri-methyl lysine 36 of histone H3 at active genes, J. Biol. Chem., 280, 17732, 10.1074/jbc.M500796200

Bannister, 2001, Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain, Nature, 410, 120, 10.1038/35065138

Bernstein, 2002, Methylation of histone H3 Lys 4 in coding regions of active genes, Proc. Natl. Acad. Sci. USA, 99, 8695, 10.1073/pnas.082249499

Bernstein, 2005, Genomic maps and comparative analysis of histone modifications in human and mouse, Cell, 120, 169, 10.1016/j.cell.2005.01.001

Bernstein, 2006, A bivalent chromatin structure marks key developmental genes in embryonic stem cells, Cell, 125, 315, 10.1016/j.cell.2006.02.041

Bernstein, 2007, The mammalian epigenome, Cell, 128, 669, 10.1016/j.cell.2007.01.033

Boyer, 2006, Polycomb complexes repress developmental regulators in murine embryonic stem cells, Nature, 441, 349, 10.1038/nature04733

Bruce, 2005, The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken, Nucleic Acids Res., 33, 5633, 10.1093/nar/gki874

Cheng, 2005, Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution, Science, 308, 1149, 10.1126/science.1108625

Craig, 1993, Chromosome bands – flavours to savour, Bioessays, 15, 349, 10.1002/bies.950150510

Crawford, 2006, Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS), Genome Res., 16, 123, 10.1101/gr.4074106

Gaszner, 2006, Insulators: exploiting transcriptional and epigenetic mechanisms, Nat. Rev. Genet., 7, 703, 10.1038/nrg1925

Guillemette, 2006, Reuniting the contrasting functions of H2A.Z, Biochem Cell Biol, 84, 528, 10.1139/o06-077

Hatton, 2006, A distal conserved sequence element controls Ifng gene expression by T cells and NK cells, Immunity, 25, 717, 10.1016/j.immuni.2006.09.007

Heintzman, 2007, Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome, Nat. Genet., 39, 311, 10.1038/ng1966

Huang, 2005, Methylation of histone H4 by arginine methyltransferase PRMT1 is essential in vivo for many subsequent histone modifications, Genes Dev., 19, 1885, 10.1101/gad.1333905

Kent, 2002, The Human Genome Browser at UCSC, Genome Res., 12, 996, 10.1101/gr.229102

Kim, 2005, A high-resolution map of active promoters in the human genome, Nature, 436, 876, 10.1038/nature03877

Kim, 2007, Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome, Cell, 128, 1231, 10.1016/j.cell.2006.12.048

Kouzarides, 2007, Chromatin modifications and their function, Cell, 128, 693, 10.1016/j.cell.2007.02.005

Lee, 2002, Synergy among nuclear receptor coactivators: selective requirement for protein methyltransferase and acetyltransferase activities, Mol. Cell. Biol., 22, 3621, 10.1128/MCB.22.11.3621-3632.2002

Lee, 2004, Evidence for nucleosome depletion at active regulatory regions genome-wide, Nat. Genet., 36, 900, 10.1038/ng1400

Lee, 2006, Control of developmental regulators by Polycomb in human embryonic stem cells, Cell, 125, 301, 10.1016/j.cell.2006.02.043

Liu, 2005, Single-nucleosome mapping of histone modifications in S. cerevisiae, PLoS Biol., 3, e328, 10.1371/journal.pbio.0030328

Loots, 2000, Identification of a coordinate regulator of interleukins 4, 13 and 5 by cross-species sequence comparisons, Science, 288, 136, 10.1126/science.288.5463.136

Meneghini, 2003, Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin, Cell, 112, 725, 10.1016/S0092-8674(03)00123-5

Miller, 2004, Comparative genomics, Annu. Rev. Genomics Hum. Genet., 5, 15, 10.1146/annurev.genom.5.061903.180057

Mito, 2007, Histone replacement marks the boundaries of cis-regulatory domains, Science, 315, 1408, 10.1126/science.1134004

Okada, 2005, hDOT1L links histone methylation to leukemogenesis, Cell, 121, 167, 10.1016/j.cell.2005.02.020

Pennacchio, 2001, Genomic strategies to identify mammalian regulatory sequences, Nat. Rev. Genet., 2, 100, 10.1038/35052548

Peters, 2003, Partitioning and plasticity of repressive histone methylation states in mammalian chromatin, Mol. Cell, 12, 1577, 10.1016/S1097-2765(03)00477-5

Pokholok, 2005, Genome-wide map of nucleosome acetylation and methylation in yeast, Cell, 122, 517, 10.1016/j.cell.2005.06.026

Raisner, 2005, Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin, Cell, 123, 233, 10.1016/j.cell.2005.10.002

Rangasamy, 2003, Pericentric heterochromatin becomes enriched with H2A.Z during early mammalian development, EMBO J., 22, 1599, 10.1093/emboj/cdg160

Roh, 2005, Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping, Genes Dev., 19, 542, 10.1101/gad.1272505

Roh, 2004, High-resolution genome-wide mapping of histone modifications, Nat. Biotechnol., 22, 1013, 10.1038/nbt990

Roh, 2006, The genomic landscape of histone modifications in human T cells, Proc. Natl. Acad. Sci. USA, 103, 15782, 10.1073/pnas.0607617103

Roh, 2007, Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns, Genome Res., 17, 74, 10.1101/gr.5767907

Schotta, 2004, A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin, Genes Dev., 18, 1251, 10.1101/gad.300704

Schubeler, 2004, The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote, Genes Dev., 18, 1263, 10.1101/gad.1198204

Sekinger, 2005, Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast, Mol. Cell, 18, 735, 10.1016/j.molcel.2005.05.003

Shnyreva, 2004, Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cells, Proc. Natl. Acad. Sci. USA, 101, 12622, 10.1073/pnas.0400849101

Sims, 2006, A trans-tail histone code defined by monomethylated H4 Lys-20 and H3 Lys-9 demarcates distinct regions of silent chromatin, J. Biol. Chem., 281, 12760, 10.1074/jbc.M513462200

Squazzo, 2006, Suz12 binds to silenced regions of the genome in a cell-type-specific manner, Genome Res., 16, 890, 10.1101/gr.5306606

Strahl, 2002, Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression, Mol. Cell. Biol., 22, 1298, 10.1128/MCB.22.5.1298-1306.2002

Su, 2004, A gene atlas of the mouse and human protein-encoding transcriptomes, Proc. Natl. Acad. Sci. USA, 101, 6062, 10.1073/pnas.0400782101

Talasz, 2005, Histone H4-lysine 20 monomethylation is increased in promoter and coding -regions of active genes and correlates with hyperacetylation, J. Biol. Chem., 280, 38814, 10.1074/jbc.M505563200

Vakoc, 2006, Profile of histone lysine methylation across transcribed mammalian chromatin, Mol. Cell. Biol., 26, 9185, 10.1128/MCB.01529-06

Yuan, 2005, Genome-scale identification of nucleosome positions in S. cerevisiae, Science, 309, 626, 10.1126/science.1112178

Zhang, 2006, Chromatin structural elements and chromosomal translocations in leukemia, DNA Repair (Amst.), 5, 1282, 10.1016/j.dnarep.2006.05.020

Zhang, 2006, Gene sequence signatures revealed by mining the UniGene affiliation network, Bioinformatics, 22, 385, 10.1093/bioinformatics/bti796