Unique Features of Long Non-coding RNA Biogenesis and Function

Overview

Journal Nat Rev Genet

Specialty Genetics

Date 2015 Dec 16

PMID 26666209

Citations 1948

Authors

Jeffrey J Quinn

Howard Y Chang

Affiliations

Soon will be listed here.

Abstract

Long non-coding RNAs (lncRNAs) are a diverse class of RNAs that engage in numerous biological processes across every branch of life. Although initially discovered as mRNA-like transcripts that do not encode proteins, recent studies have revealed features of lncRNAs that further distinguish them from mRNAs. In this Review, we describe special events in the lifetimes of lncRNAs - before, during and after transcription - and discuss how these events ultimately shape the unique characteristics and functional roles of lncRNAs.

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References

Ulitsky I, Bartel D . lincRNAs: genomics, evolution, and mechanisms. Cell. 2013; 154(1):26-46. PMC: 3924787. DOI: 10.1016/j.cell.2013.06.020. View

Beltran M, Puig I, Pena C, Garcia J, Alvarez A, Pena R . A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev. 2008; 22(6):756-69. PMC: 2275429. DOI: 10.1101/gad.455708. View

Tian D, Sun S, Lee J . The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell. 2010; 143(3):390-403. PMC: 2994261. DOI: 10.1016/j.cell.2010.09.049. View

Coccia E, Cicala C, Charlesworth A, Ciccarelli C, Rossi G, Philipson L . Regulation and expression of a growth arrest-specific gene (gas5) during growth, differentiation, and development. Mol Cell Biol. 1992; 12(8):3514-21. PMC: 364604. DOI: 10.1128/mcb.12.8.3514-3521.1992. View

Brown J, Valenstein M, Yario T, Tycowski K, Steitz J . Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MENβ noncoding RNAs. Proc Natl Acad Sci U S A. 2012; 109(47):19202-7. PMC: 3511071. DOI: 10.1073/pnas.1217338109. View

Kurihara Y, Matsui A, Hanada K, Kawashima M, Ishida J, Morosawa T . Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis. Proc Natl Acad Sci U S A. 2009; 106(7):2453-8. PMC: 2650177. DOI: 10.1073/pnas.0808902106. View

Carninci P, Kasukawa T, Katayama S, Gough J, Frith M, Maeda N . The transcriptional landscape of the mammalian genome. Science. 2005; 309(5740):1559-63. DOI: 10.1126/science.1112014. View

Zhang Y, Zhang X, Chen T, Xiang J, Yin Q, Xing Y . Circular intronic long noncoding RNAs. Mol Cell. 2013; 51(6):792-806. DOI: 10.1016/j.molcel.2013.08.017. View

Thiebaut M, Kisseleva-Romanova E, Rougemaille M, Boulay J, Libri D . Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance. Mol Cell. 2006; 23(6):853-64. DOI: 10.1016/j.molcel.2006.07.029. View

10.

Tay Y, Rinn J, Pandolfi P . The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014; 505(7483):344-52. PMC: 4113481. DOI: 10.1038/nature12986. View

11.

Colak D, Zaninovic N, Cohen M, Rosenwaks Z, Yang W, Gerhardt J . Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in fragile X syndrome. Science. 2014; 343(6174):1002-5. PMC: 4357282. DOI: 10.1126/science.1245831. View

12.

Di Croce L, Helin K . Transcriptional regulation by Polycomb group proteins. Nat Struct Mol Biol. 2013; 20(10):1147-55. DOI: 10.1038/nsmb.2669. View

13.

Diederichs S . The four dimensions of noncoding RNA conservation. Trends Genet. 2014; 30(4):121-3. DOI: 10.1016/j.tig.2014.01.004. View

14.

Lyle R, Watanabe D, te Vruchte D, Lerchner W, Smrzka O, Wutz A . The imprinted antisense RNA at the Igf2r locus overlaps but does not imprint Mas1. Nat Genet. 2000; 25(1):19-21. DOI: 10.1038/75546. View

15.

Lin S, Youngson N, Takada S, Seitz H, Reik W, Paulsen M . Asymmetric regulation of imprinting on the maternal and paternal chromosomes at the Dlk1-Gtl2 imprinted cluster on mouse chromosome 12. Nat Genet. 2003; 35(1):97-102. DOI: 10.1038/ng1233. View

16.

Batista P, Chang H . Long noncoding RNAs: cellular address codes in development and disease. Cell. 2013; 152(6):1298-307. PMC: 3651923. DOI: 10.1016/j.cell.2013.02.012. View

17.

Conrad N, Steitz J . A Kaposi's sarcoma virus RNA element that increases the nuclear abundance of intronless transcripts. EMBO J. 2005; 24(10):1831-41. PMC: 1142595. DOI: 10.1038/sj.emboj.7600662. View

18.

Wang K, Yang Y, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y . A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature. 2011; 472(7341):120-4. PMC: 3670758. DOI: 10.1038/nature09819. View

19.

Lim C, Kelley R . Autoregulation of the Drosophila Noncoding roX1 RNA Gene. PLoS Genet. 2012; 8(3):e1002564. PMC: 3305356. DOI: 10.1371/journal.pgen.1002564. View

20.

van Dijk E, Chen C, dAubenton-Carafa Y, Gourvennec S, Kwapisz M, Roche V . XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast. Nature. 2011; 475(7354):114-7. DOI: 10.1038/nature10118. View