1. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
2. Department of Biology,
3. The Koch Institute for Integrative Cancer Research,
4. Division of Health Sciences and Technology, and,
5. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
6. Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
7. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02114, USA
8. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
9. Center for Immunology and Inflammatory Diseases,
10. Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
11. Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
12. These authors contributed equally to this work.

Correspondence to: John L. Rinn^1,6,11,12 Correspondence and requests for materials should be addressed to J.L.R. (Email: jrinn@broad.mit.edu).

Abstract

There is growing recognition that mammalian cells produce many thousands of large intergenic transcripts^{1, 2, 3, 4}. 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^{5, 6}. 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 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, NFB, 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.

MORE ARTICLES LIKE THIS

These links to content published by NPG are automatically generated.