Prediction of transposable element derived enhancers using chromatin modification profiles
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 transp...
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| Veröffentlicht in: | PloS one 2011-11, Vol.6 (11), p.e27513-e27513 |
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| creator | Huda, Ahsan Tyagi, Eishita Mariño-Ramírez, Leonardo Bowen, Nathan J Jjingo, Daudi Jordan, I King |
| description | 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. |
| doi_str_mv | 10.1371/journal.pone.0027513 |
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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><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0027513</identifier><identifier>PMID: 22087331</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Bioinformatics ; Biology ; Biotechnology ; Cell Line ; Cell lines ; Chromatin ; Chromatin - metabolism ; Cluster analysis ; Computer applications ; Deoxyribonucleic acid ; DNA ; DNA Transposable Elements ; Enhancers ; Epigenesis, Genetic ; Epigenetic inheritance ; Erythroid Precursor Cells ; Gene Expression ; Gene sequencing ; Genes ; Genome, Human ; Genomes ; Genomics ; Histones ; Humans ; Information retrieval ; K562 Cells ; Methods ; Predictions ; Regulatory mechanisms (biology) ; Stem cells ; Transcription Factors ; Transposons</subject><ispartof>PloS one, 2011-11, Vol.6 (11), p.e27513-e27513</ispartof><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>2011 Huda et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Huda et al. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c691t-f1a7e87769c16a309b60324e320a5aab68ad985acb7c17324678792c1886907f3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3210180/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3210180/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22087331$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Dalal, Yamini</contributor><creatorcontrib>Huda, Ahsan</creatorcontrib><creatorcontrib>Tyagi, Eishita</creatorcontrib><creatorcontrib>Mariño-Ramírez, Leonardo</creatorcontrib><creatorcontrib>Bowen, Nathan J</creatorcontrib><creatorcontrib>Jjingo, Daudi</creatorcontrib><creatorcontrib>Jordan, I King</creatorcontrib><title>Prediction of transposable element derived enhancers using chromatin modification profiles</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>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. 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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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22087331</pmid><doi>10.1371/journal.pone.0027513</doi><tpages>e27513</tpages><oa>free_for_read</oa></addata></record> |
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| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Bioinformatics Biology Biotechnology Cell Line Cell lines Chromatin Chromatin - metabolism Cluster analysis Computer applications Deoxyribonucleic acid DNA DNA Transposable Elements Enhancers Epigenesis, Genetic Epigenetic inheritance Erythroid Precursor Cells Gene Expression Gene sequencing Genes Genome, Human Genomes Genomics Histones Humans Information retrieval K562 Cells Methods Predictions Regulatory mechanisms (biology) Stem cells Transcription Factors Transposons |
| title | Prediction of transposable element derived enhancers using chromatin modification profiles |
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