Prediction of transposable element derived enhancers using chromatin modification profiles

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dc.contributor.authorHuda, Ahsan
dc.contributor.authorTyagi, Eishita
dc.contributor.authorMarino-Ramırez, Leonardo
dc.contributor.authorBowen, Nathan J.
dc.contributor.authorJjingo, Daudi
dc.contributor.authorKing Jordan, I.
dc.date.accessioned2018-06-26T15:12:24Z
dc.date.accessioned2021-12-21T08:58:56Z
dc.date.available2018-06-26T15:12:24Z
dc.date.available2021-12-21T08:58:56Z
dc.date.issued2011-11-07
dc.descriptionThe definitive version of this Open Access article was published by PLoS ONE 6(11): e27513. doi:10.1371/journal.pone.0027513en_US
dc.description.abstractExperimentally 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.en_US
dc.identifier.citationHuda A, Tyagi E, Marino-Ramırez 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.0027513en_US
dc.identifier.issn1553-7404
dc.identifier.urihttps://hdl.handle.net/20.500.11951/248
dc.language.isoenen_US
dc.publisherPLoS ONE (Public Library of Science)en_US
dc.rightsAttribution 3.0 United States*
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/us/*
dc.subjectGenome, human - Transposable elementsen_US
dc.subjectChromatin profilesen_US
dc.subjectTransposable elements enhancers - Geneticsen_US
dc.titlePrediction of transposable element derived enhancers using chromatin modification profilesen_US
dc.typeArticleen_US
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