Cargando…
Epigenetic regulation of human cis-natural antisense transcripts
Mammalian genomes encode numerous cis-natural antisense transcripts (cis-NATs). The extent to which these cis-NATs are actively regulated and ultimately functionally relevant, as opposed to transcriptional noise, remains a matter of debate. To address this issue, we analyzed the chromatin environmen...
Autores principales: | , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2012
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287164/ https://www.ncbi.nlm.nih.gov/pubmed/22371288 http://dx.doi.org/10.1093/nar/gkr1010 |
_version_ | 1782224625865850880 |
---|---|
author | Conley, Andrew B. King Jordan, I. |
author_facet | Conley, Andrew B. King Jordan, I. |
author_sort | Conley, Andrew B. |
collection | PubMed |
description | Mammalian genomes encode numerous cis-natural antisense transcripts (cis-NATs). The extent to which these cis-NATs are actively regulated and ultimately functionally relevant, as opposed to transcriptional noise, remains a matter of debate. To address this issue, we analyzed the chromatin environment and RNA Pol II binding properties of human cis-NAT promoters genome-wide. Cap analysis of gene expression data were used to identify thousands of cis-NAT promoters, and profiles of nine histone modifications and RNA Pol II binding for these promoters in ENCODE cell types were analyzed using chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Active cis-NAT promoters are enriched with activating histone modifications and occupied by RNA Pol II, whereas weak cis-NAT promoters are depleted for both activating modifications and RNA Pol II. The enrichment levels of activating histone modifications and RNA Pol II binding show peaks centered around cis-NAT transcriptional start sites, and the levels of activating histone modifications at cis-NAT promoters are positively correlated with cis-NAT expression levels. Cis-NAT promoters also show highly tissue-specific patterns of expression. These results suggest that human cis-NATs are actively transcribed by the RNA Pol II and that their expression is epigenetically regulated, prerequisites for a functional potential for many of these non-coding RNAs. |
format | Online Article Text |
id | pubmed-3287164 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-32871642012-02-27 Epigenetic regulation of human cis-natural antisense transcripts Conley, Andrew B. King Jordan, I. Nucleic Acids Res Computational Biology Mammalian genomes encode numerous cis-natural antisense transcripts (cis-NATs). The extent to which these cis-NATs are actively regulated and ultimately functionally relevant, as opposed to transcriptional noise, remains a matter of debate. To address this issue, we analyzed the chromatin environment and RNA Pol II binding properties of human cis-NAT promoters genome-wide. Cap analysis of gene expression data were used to identify thousands of cis-NAT promoters, and profiles of nine histone modifications and RNA Pol II binding for these promoters in ENCODE cell types were analyzed using chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Active cis-NAT promoters are enriched with activating histone modifications and occupied by RNA Pol II, whereas weak cis-NAT promoters are depleted for both activating modifications and RNA Pol II. The enrichment levels of activating histone modifications and RNA Pol II binding show peaks centered around cis-NAT transcriptional start sites, and the levels of activating histone modifications at cis-NAT promoters are positively correlated with cis-NAT expression levels. Cis-NAT promoters also show highly tissue-specific patterns of expression. These results suggest that human cis-NATs are actively transcribed by the RNA Pol II and that their expression is epigenetically regulated, prerequisites for a functional potential for many of these non-coding RNAs. Oxford University Press 2012-02 2012-02-25 /pmc/articles/PMC3287164/ /pubmed/22371288 http://dx.doi.org/10.1093/nar/gkr1010 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Computational Biology Conley, Andrew B. King Jordan, I. Epigenetic regulation of human cis-natural antisense transcripts |
title | Epigenetic regulation of human cis-natural antisense transcripts |
title_full | Epigenetic regulation of human cis-natural antisense transcripts |
title_fullStr | Epigenetic regulation of human cis-natural antisense transcripts |
title_full_unstemmed | Epigenetic regulation of human cis-natural antisense transcripts |
title_short | Epigenetic regulation of human cis-natural antisense transcripts |
title_sort | epigenetic regulation of human cis-natural antisense transcripts |
topic | Computational Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287164/ https://www.ncbi.nlm.nih.gov/pubmed/22371288 http://dx.doi.org/10.1093/nar/gkr1010 |
work_keys_str_mv | AT conleyandrewb epigeneticregulationofhumancisnaturalantisensetranscripts AT kingjordani epigeneticregulationofhumancisnaturalantisensetranscripts |