title: Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells.
abstract: Epigenetic modifications are crucial for proper lineage specification and embryo development. To explore the chromatin modification landscapes in human ES cells, we profiled two histone modifications, H3K4me3 and H3K27me3, by ChIP coupled with the paired-end ditags sequencing strategy. H3K4me3 was found to be a prevalent mark and occurred in close proximity to the promoters of two-thirds of total human genes. Among the H3K27me3 loci identified, 56% are associated with promoters and the vast majority of them are comodified by H3K4me3. By deep-transcript digital counting, 80% of H3K4me3 and 36% of comodified promoters were found to be transcribed. Remarkably, we observed that different combinations of histone methylations are associated with genes from distinct functional categories. These global histone methylation maps provide an epigenetic framework that enables the discovery of novel transcriptional networks and delineation of different genetic compartments of the pluripotent cell genome.
authors: Genome Technology and Biology Group, Genome Institute of Singapore, 138672, Singapore.
authors: Xiao Dong
authors: XD
authors: Zhao
authors: Xu
authors: X
authors: Han
authors: Joon Lin
authors: JL
authors: Chew
authors: Jun
authors: J
authors: Liu
authors: Kuo Ping
authors: KP
authors: Chiu
authors: Andre
authors: A
authors: Choo
authors: Yuriy L
authors: YL
authors: Orlov
authors: Wing-Kin
authors: WK
authors: Sung
authors: Atif
authors: A
authors: Shahab
authors: Vladimir A
authors: VA
authors: Kuznetsov
authors: Guillaume
authors: G
authors: Bourque
authors: Steve
authors: S
authors: Oh
authors: Yijun
authors: Y
authors: Ruan
authors: Huck-Hui
authors: HH
authors: Ng
authors: Chia-Lin
authors: CL
authors: Wei
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D017124:Conserved Sequence; D021901:DNA, Intergenic / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D020869:Gene Expression Profiling; D015894:Genome, Human / Q000235:genetics*; D006657:Histones / Q000378:metabolism*; D006801:Humans; D008239:Lysine / Q000378:metabolism*; D008745:Methylation; D051379:Mice; D046988:Proteasome Endopeptidase Complex / Q000235:genetics; D021381:Protein Transport; D014158:Transcription, Genetic; D015854:Up-Regulation / Q000235:genetics; D014714:Vertebrates / Q000235:genetics
chemical_list: D021901:DNA, Intergenic; D004268:DNA-Binding Proteins; D006657:Histones; D046988:Proteasome Endopeptidase Complex; D008239:Lysine