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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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2011-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0027513&type=printable |
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| author | Ahsan Huda Eishita Tyagi Leonardo Mariño-Ramírez Nathan J Bowen Daudi Jjingo I King Jordan |
| author_facet | Ahsan Huda Eishita Tyagi Leonardo Mariño-Ramírez Nathan J Bowen Daudi Jjingo I King Jordan |
| author_sort | Ahsan Huda |
| collection | DOAJ |
| 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. |
| format | Article |
| id | doaj-art-147dc18a8fff4fecb434fe18fa2d5b50 |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2011-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-147dc18a8fff4fecb434fe18fa2d5b502025-08-20T03:25:07ZengPublic Library of Science (PLoS)PLoS ONE1932-62032011-01-01611e2751310.1371/journal.pone.0027513Prediction of transposable element derived enhancers using chromatin modification profiles.Ahsan HudaEishita TyagiLeonardo Mariño-RamírezNathan J BowenDaudi JjingoI King JordanExperimentally 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.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0027513&type=printable |
| spellingShingle | Ahsan Huda Eishita Tyagi Leonardo Mariño-Ramírez Nathan J Bowen Daudi Jjingo I King Jordan Prediction of transposable element derived enhancers using chromatin modification profiles. PLoS ONE |
| title | Prediction of transposable element derived enhancers using chromatin modification profiles. |
| title_full | Prediction of transposable element derived enhancers using chromatin modification profiles. |
| title_fullStr | Prediction of transposable element derived enhancers using chromatin modification profiles. |
| title_full_unstemmed | Prediction of transposable element derived enhancers using chromatin modification profiles. |
| title_short | Prediction of transposable element derived enhancers using chromatin modification profiles. |
| title_sort | prediction of transposable element derived enhancers using chromatin modification profiles |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0027513&type=printable |
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