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Zhibin Wang1,5, Chongzhi Zang4,5, Jeffrey A. Rosenfeld2,3,5, Dustin E. Schones1, Artem Barski1, Suresh Cuddapah1, Kairong Cui1, Tae-Young Roh1, Weiqun Peng4, Michael Q. Zhang2 and Keji Zhao1,6

1 Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892
2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
3 Department of Biology, New York University
4 Department of Physics, The George Washington University, D.C.
5 These authors made equal contributions to this work.
6 Corresponding author


Histones are characterized by numerous post-translational modifications that influence gene transcription. However, due to the lack of global distribution data in higher eukaryotic systems, it remains to be determined the extent to which gene-specific combinatorial patterns of histone modifications exist. Here we report the patterns derived from analyzing 38 histone modifications in human CD4+ T cells. Our data indicate that a large number of patterns are associated with promoters and enhancers. In particular, we identify a common modification module consisting of 17 modifications at 3,090 promoters. These modifications tend to colocalize in the genome and correlate with each other at an individual nucleosome level. Genes associated with this module tend to have higher expression levels and addition of more modifications to this module is associated with further increased expression. Our data suggest that these histone modifications may act cooperatively to prepare chromatin for transcriptional activation.


Data Set Tag coordinate bed file Summary bed file UCSC track
H3K4ac H3K4ac H3K4ac H3K4ac
H3K9ac H3K9ac H3K9ac H3K9ac
H3K14ac H3K14ac H3K14ac H3K14ac
H3K18ac H3K18ac H3K18ac H3K18ac
H3K23ac H3K23ac H3K23ac H3K23ac
H3K27ac H3K27ac H3K27ac H3K27ac
H3K36ac H3K36ac H3K36ac H3K36ac
H4K5ac H4K5ac H4K5ac H4K5ac
H4K8ac H4K8ac H4K8ac H4K8ac
H4K12ac H4K12ac H4K12ac H4K12ac
H4K16ac H4K16ac H4K16ac H4K16ac
H4K91ac H4K91ac H4K91ac H4K91ac
H2AK5ac H2AK5ac H2AK5ac H2AK5ac
H2AK9ac H2AK9ac H2AK9ac H2AK9ac
H2BK5ac H2BK5ac H2BK5ac H2BK5ac
H2BK12ac H2BK12ac H2BK12ac H2BK12ac
H2BK20ac H2BK20ac H2BK20ac H2BK20ac
H2BK120ac H2BK120ac H2BK120ac H2BK120ac

Information on file formats

Tag coordinate bed files -- contain coordinates for all uniquely mapped reads for each experiment. Each line is in the format:

chromosome start coordinate end coordinate match type strand

Summary bed files -- Bed files displaying the number of uniquely mapped reads in 200 bp windows. All read start coordinates are adjusted by 75 bp in the direction of the strand they map to before summing is done.

UCSC custom tracks -- Automatic linking of summary bed files, or nucleosome score files to the UCSC Genome Browser to create custom tracks.

(Note: all coordinates are from the Human Mar. 2006 (hg18) assembly)

Data corresponding to this project have been deposited in the NCBI Short Read Archive with accession number SRA000287