Document Detail


Epigenetic regulation of human cis-natural antisense transcripts.
MedLine Citation:
PMID:  22371288     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Andrew B Conley; I King Jordan
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Nucleic acids research     Volume:  40     ISSN:  1362-4962     ISO Abbreviation:  Nucleic Acids Res.     Publication Date:  2012 Feb 
Date Detail:
Created Date:  2012-02-28     Completed Date:  2012-04-23     Revised Date:  2013-06-26    
Medline Journal Info:
Nlm Unique ID:  0411011     Medline TA:  Nucleic Acids Res     Country:  England    
Other Details:
Languages:  eng     Pagination:  1438-45     Citation Subset:  IM    
Affiliation:
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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MeSH Terms
Descriptor/Qualifier:
Chromatin / metabolism
Epigenesis, Genetic*
Histones / metabolism
Humans
Promoter Regions, Genetic
RNA Polymerase II / metabolism
RNA, Antisense / biosynthesis,  genetics*
Transcription Initiation Site
Transcription, Genetic
Chemical
Reg. No./Substance:
0/Chromatin; 0/Histones; 0/RNA, Antisense; EC 2.7.7.-/RNA Polymerase II
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