Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells.
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.
Zhao
Xiao Dong
XD
Genome Technology and Biology Group, Genome Institute of Singapore, 138672, Singapore.
Han
Xu
X
Chew
Joon Lin
JL
Liu
Jun
J
Chiu
Kuo Ping
KP
Choo
Andre
A
Orlov
Yuriy L
YL
Sung
Wing-Kin
WK
Shahab
Atif
A
Kuznetsov
Vladimir A
VA
Bourque
Guillaume
G
Oh
Steve
S
Ruan
Yijun
Y
Ng
Huck-Hui
HH
Wei
Chia-Lin
CL
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
D021901:DNA, Intergenic; D004268:DNA-Binding Proteins; D006657:Histones; D046988:Proteasome Endopeptidase Complex; D008239:Lysine