title: Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.
abstract: There is growing recognition that mammalian cells produce many thousands of large intergenic transcripts. However, the functional significance of these transcripts has been particularly controversial. Although there are some well-characterized examples, most (>95%) show little evidence of evolutionary conservation and have been suggested to represent transcriptional noise. Here we report a new approach to identifying large non-coding RNAs using chromatin-state maps to discover discrete transcriptional units intervening known protein-coding loci. Our approach identified approximately 1,600 large multi-exonic RNAs across four mouse cell types. In sharp contrast to previous collections, these large intervening non-coding RNAs (lincRNAs) show strong purifying selection in their genomic loci, exonic sequences and promoter regions, with greater than 95% showing clear evolutionary conservation. We also developed a functional genomics approach that assigns putative functions to each lincRNA, demonstrating a diverse range of roles for lincRNAs in processes from embryonic stem cell pluripotency to cell proliferation. We obtained independent functional validation for the predictions for over 100 lincRNAs, using cell-based assays. In particular, we demonstrate that specific lincRNAs are transcriptionally regulated by key transcription factors in these processes such as p53, NFkappaB, Sox2, Oct4 (also known as Pou5f1) and Nanog. Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes.
authors.affiliation: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
authors.forename: Mitchell
authors.initials: M
authors.lastname: Guttman
authors.forename: Ido
authors.initials: I
authors.lastname: Amit
authors.forename: Manuel
authors.initials: M
authors.lastname: Garber
authors.forename: Courtney
authors.initials: C
authors.lastname: French
authors.forename: Michael F
authors.initials: MF
authors.lastname: Lin
authors.forename: David
authors.initials: D
authors.lastname: Feldser
authors.forename: Maite
authors.initials: M
authors.lastname: Huarte
authors.forename: Or
authors.initials: O
authors.lastname: Zuk
authors.forename: Bryce W
authors.initials: BW
authors.lastname: Carey
authors.forename: John P
authors.initials: JP
authors.lastname: Cassady
authors.forename: Moran N
authors.initials: MN
authors.lastname: Cabili
authors.forename: Rudolf
authors.initials: R
authors.lastname: Jaenisch
authors.forename: Tarjei S
authors.initials: TS
authors.lastname: Mikkelsen
authors.forename: Tyler
authors.initials: T
authors.lastname: Jacks
authors.forename: Nir
authors.initials: N
authors.lastname: Hacohen
authors.forename: Bradley E
authors.initials: BE
authors.lastname: Bernstein
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
authors.forename: John L
authors.initials: JL
authors.lastname: Rinn
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
mesh_terms: D000818:Animals; D001483:Base Sequence; D002478:Cells, Cultured; D002843:Chromatin / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D021901:DNA, Intergenic; D005091:Exons / Q000235:genetics; D008322:Mammals / Q000235:genetics*; D051379:Mice; D011401:Promoter Regions, Genetic / Q000235:genetics; D012313:RNA / Q000235:genetics*; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D002843:Chromatin; D021901:DNA, Intergenic; D014157:Transcription Factors; D012313:RNA