Discovery and Annotation of Functional Chromatin Signatures in the Human Genome

Abstract

Transcriptional regulation in human cells is a complex process involving a multitude of regulatory elements encoded by the genome. Recent studies have shown that distinct chromatin signatures mark a variety of functional genomic elements and that subtle variations of these signatures mark elements with different functions. To identify novel chromatin signatures in the human genome, we apply a de novo pattern-finding algorithm to genome-wide maps of histone modifications. We recover previously known chromatin signatures associated with promoters and enhancers. We also observe several chromatin signatures with strong enrichment of H3K36me3 marking exons. Closer examination reveals that H3K36me3 is found on well-positioned nucleosomes at exon 5′ ends, and that this modification is a global mark of exon expression that also correlates with alternative splicing. Additionally, we observe strong enrichment of H2BK5me1 and H4K20me1 at highly expressed exons near the 5′ end, in contrast to the opposite distribution of H3K36me3-marked exons. Finally, we also recover frequently occurring chromatin signatures displaying enrichment of repressive histone modifications. These signatures mark distinct repeat sequences and are associated with distinct modes of gene repression. Together, these results highlight the rich information embedded in the human epigenome and underscore its value in studying gene regulation. Recent studies have observed that histone tails can be modified in a variety of ways. Analyzing a collection of 21 histone modifications, we attempted to determine what common signatures are associated with different classes of regulatory elements and whether they mark places of distinct function. Indeed, at promoters, we identified a number of distinct signatures, each associated with a different class of expressed and functional genes. We also observed several unexpected signatures marking exons that directly correlate with the expression of exons. Finally, we recovered many places marked by two distinct repressive modifications, and showed that they mark distinct populations of repetitive elements associated with distinct modes of gene repression. Together, these results highlight the rich information embedded in the human epigenome and underscore its value in studying gene regulation.