Prediction of Transposable Element Derived Enhancers Using Chromatin Modification Profiles
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Date
2011
Journal Title
Journal ISSN
Volume Title
Publisher
PLoS ONE
Abstract
Experimentally characterized enhancer regions have previously been shown to display specific patterns of enrichment for
several different histone modifications. We modelled these enhancer chromatin profiles in the human genome and used
them to guide the search for novel enhancers derived from transposable element (TE) sequences. To do this, a
computational approach was taken to analyze the genome-wide histone modification landscape characterized by the
ENCODE project in two human hematopoietic cell types, GM12878 and K562. We predicted the locations of 2,107 and 1,448
TE-derived enhancers in the GM12878 and K562 cell lines respectively. A vast majority of these putative enhancers are
unique to each cell line; only 3.5% of the TE-derived enhancers are shared between the two. We evaluated the functional
effect of TE-derived enhancers by associating them with the cell-type specific expression of nearby genes, and found that
the number of TE-derived enhancers is strongly positively correlated with the expression of nearby genes in each cell line.
Furthermore, genes that are differentially expressed between the two cell lines also possess a divergent number of TE derived
enhancers in their vicinity. As such, genes that are up-regulated in the GM12878 cell line and down-regulated in
K562 have significantly more TE-derived enhancers in their vicinity in the GM12878 cell line and vice versa. These data
indicate that human TE-derived sequences are likely to be involved in regulating cell-type specific gene expression on a
broad scale and suggest that the enhancer activity of TE-derived sequences is mediated by epigenetic regulatory
mechanisms.
Description
Keywords
Element, Chromatin Modification Profiles
Citation
Huda A, Tyagi E, Marin˜o-Ramı´rez L, Bowen NJ, Jjingo D, et al. (2011) Prediction of Transposable Element Derived Enhancers Using Chromatin Modification Profiles. PLoS ONE 6(11): e27513. doi:10.1371/journal.pone.0027513