title: Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs.
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.
authors.forename: Ana C
authors.initials: AC
authors.lastname: Marques
authors.forename: Jim
authors.initials: J
authors.lastname: Hughes
authors.forename: Bryony
authors.initials: B
authors.lastname: Graham
authors.forename: Monika S
authors.initials: MS
authors.lastname: Kowalczyk
authors.forename: Doug R
authors.initials: DR
authors.lastname: Higgs
authors.forename: Chris P
authors.initials: CP
authors.lastname: Ponting
mesh_terms: D000818:Animals; D002843:Chromatin / Q000737:chemistry* / Q000235:genetics; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D056426:Genetic Loci; D006657:Histones / Q000235:genetics; D051379:Mice; D008810:Mice, Inbred C57BL; D011401:Promoter Regions, Genetic; D017434:Protein Structure, Tertiary; D062085:RNA, Long Noncoding / Q000737:chemistry* / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D017422:Sequence Analysis, DNA; D024363:Transcription Initiation Site; D059467:Transcriptome
chemical_list: D002843:Chromatin; D006657:Histones; D062085:RNA, Long Noncoding; D012333:RNA, Messenger