Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs.

Details

Ressource 1Download: BIB_E59A3ACE6418.P001.pdf (1634.12 [Ko])
State: Public
Version: author
Serval ID
serval:BIB_E59A3ACE6418
Type
Article: article from journal or magazin.
Collection
Publications
Title
Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs.
Journal
Genome Biology
Author(s)
Marques A.C., Hughes J., Graham B., Kowalczyk M.S., Higgs D.R., Ponting C.P.
ISSN
1474-760X (Electronic)
ISSN-L
1474-7596
Publication state
Published
Issued date
2013
Volume
14
Number
11
Pages
R131
Language
english
Abstract
BACKGROUND: Mammalian transcriptomes contain thousands of long noncoding RNAs (lncRNAs). Some lncRNAs originate from intragenic enhancers which, when active, behave as alternative promoters producing transcripts that are processed using the canonical signals of their host gene. We have followed up this observation by analyzing intergenic lncRNAs to determine the extent to which they might also originate from intergenic enhancers.
RESULTS: We integrated high-resolution maps of transcriptional initiation and transcription to annotate a conservative set of intergenic lncRNAs expressed in mouse erythroblasts. We subclassified intergenic lncRNAs according to chromatin status at transcriptional initiation regions, defined by relative levels of histone H3K4 mono- and trimethylation. These transcripts are almost evenly divided between those arising from enhancer-associated (elncRNA) or promoter-associated (plncRNA) elements. These two classes of 5' capped and polyadenylated RNA transcripts are indistinguishable with regard to their length, number of exons or transcriptional orientation relative to their closest neighboring gene. Nevertheless, elncRNAs are more tissue-restricted, less highly expressed and less well conserved during evolution. Of considerable interest, we found that expression of elncRNAs, but not plncRNAs, is associated with enhanced expression of neighboring protein-coding genes during erythropoiesis.
CONCLUSIONS: We have determined globally the sites of initiation of intergenic lncRNAs in erythroid cells, allowing us to distinguish two similarly abundant classes of transcripts. Different correlations between the levels of elncRNAs, plncRNAs and expression of neighboring genes suggest that functional lncRNAs from the two classes may play contrasting roles in regulating the transcript abundance of local or distal loci.
Keywords
Animals, Chromatin/chemistry, Chromatin/genetics, Evolution, Molecular, Gene Expression Regulation, Genetic Loci, Histones/genetics, Mice, Mice, Inbred C57BL, Promoter Regions, Genetic, Protein Structure, Tertiary, RNA, Long Noncoding/chemistry, RNA, Long Noncoding/genetics, RNA, Messenger/genetics, Sequence Analysis, DNA, Transcription Initiation Site, Transcriptome
Pubmed
Web of science
Open Access
Yes
Create date
27/10/2014 14:44
Last modification date
20/08/2019 16:08
Usage data