Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.
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.
Guttman
Mitchell
M
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
Amit
Ido
I
Garber
Manuel
M
French
Courtney
C
Lin
Michael F
MF
Feldser
David
D
Huarte
Maite
M
Zuk
Or
O
Carey
Bryce W
BW
Cassady
John P
JP
Cabili
Moran N
MN
Jaenisch
Rudolf
R
Mikkelsen
Tarjei S
TS
Jacks
Tyler
T
Hacohen
Nir
N
Bernstein
Bradley E
BE
Kellis
Manolis
M
Regev
Aviv
A
Rinn
John L
JL
Lander
Eric S
ES
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
D002843:Chromatin; D021901:DNA, Intergenic; D014157:Transcription Factors; D012313:RNA