Histones are characterized by numerous posttranslational modifications that influence gene transcription. However, because of the lack of global distribution data in higher eukaryotic systems, the extent to which gene-specific combinatorial patterns of histone modifications exist remains to be determined. Here, we report the patterns derived from the analysis of 39 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 detected at 3,286 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, 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.
Bibliographical noteFunding Information:
We thank W. Leonard for comments. This work was supported by the Intramural Research Program of the US National Institutes of Health, National Heart, Lung, and Blood Institute (K.Z.) and by an NIH grant HG001696 (M.Q.Z.). J.A.R. is supported by an NIH training grant to New York University and a New York University McCracken Fellowship.