Decoding the Function of Nuclear Long Non-coding RNAs

Overview

Journal Curr Opin Cell Biol

Publisher Elsevier

Specialty Cell Biology

Date 2010 Apr 2

PMID 20356723

Citations 118

Authors

Ling-Ling Chen

Gordon G Carmichael

Affiliations

Soon will be listed here.

Abstract

Long non-coding RNAs (lncRNAs) are mRNA-like, non-protein-coding RNAs that are pervasively transcribed throughout eukaryotic genomes. Rather than silently accumulating in the nucleus, many of these are now known or suspected to play important roles in nuclear architecture or in the regulation of gene expression. In this review, we highlight some recent progress in how lncRNAs regulate these important nuclear processes at the molecular level.

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References

Chow J, Heard E . X inactivation and the complexities of silencing a sex chromosome. Curr Opin Cell Biol. 2009; 21(3):359-66. DOI: 10.1016/j.ceb.2009.04.012. View

Mariner P, Walters R, Espinoza C, Drullinger L, Wagner S, Kugel J . Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell. 2008; 29(4):499-509. DOI: 10.1016/j.molcel.2007.12.013. View

Bertone P, Stolc V, Royce T, Rozowsky J, Urban A, Zhu X . Global identification of human transcribed sequences with genome tiling arrays. Science. 2004; 306(5705):2242-6. DOI: 10.1126/science.1103388. View

Shamovsky I, Ivannikov M, Kandel E, Gershon D, Nudler E . RNA-mediated response to heat shock in mammalian cells. Nature. 2006; 440(7083):556-60. DOI: 10.1038/nature04518. View

Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A . Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature. 2007; 445(7128):666-70. DOI: 10.1038/nature05519. View

Zhang L, Huynh K, Lee J . Perinucleolar targeting of the inactive X during S phase: evidence for a role in the maintenance of silencing. Cell. 2007; 129(4):693-706. DOI: 10.1016/j.cell.2007.03.036. View

Wilusz J, Freier S, Spector D . 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell. 2008; 135(5):919-32. PMC: 2722846. DOI: 10.1016/j.cell.2008.10.012. View

Chen L, DeCerbo J, Carmichael G . Alu element-mediated gene silencing. EMBO J. 2008; 27(12):1694-705. PMC: 2435129. DOI: 10.1038/emboj.2008.94. View

Wang X, Arai S, Song X, Reichart D, Du K, Pascual G . Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature. 2008; 454(7200):126-30. PMC: 2823488. DOI: 10.1038/nature06992. View

10.

Guttman M, Amit I, Garber M, French C, Lin M, Feldser D . Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 2009; 458(7235):223-7. PMC: 2754849. DOI: 10.1038/nature07672. View

11.

Sasaki Y, Ideue T, Sano M, Mituyama T, Hirose T . MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci U S A. 2009; 106(8):2525-30. PMC: 2650297. DOI: 10.1073/pnas.0807899106. View

12.

Ogawa Y, Sun B, Lee J . Intersection of the RNA interference and X-inactivation pathways. Science. 2008; 320(5881):1336-41. PMC: 2584363. DOI: 10.1126/science.1157676. View

13.

He Y, Vogelstein B, Velculescu V, Papadopoulos N, Kinzler K . The antisense transcriptomes of human cells. Science. 2008; 322(5909):1855-7. PMC: 2824178. DOI: 10.1126/science.1163853. View

14.

Dinger M, Amaral P, Mercer T, Pang K, Bruce S, Gardiner B . Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 2008; 18(9):1433-45. PMC: 2527704. DOI: 10.1101/gr.078378.108. View

15.

Fox A, Lam Y, Leung A, Lyon C, Andersen J, Mann M . Paraspeckles: a novel nuclear domain. Curr Biol. 2002; 12(1):13-25. DOI: 10.1016/s0960-9822(01)00632-7. View

16.

Nagano T, Mitchell J, Sanz L, Pauler F, Ferguson-Smith A, Feil R . The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science. 2008; 322(5908):1717-20. DOI: 10.1126/science.1163802. View

17.

Clemson C, Hutchinson J, Sara S, Ensminger A, Fox A, Chess A . An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell. 2009; 33(6):717-26. PMC: 2696186. DOI: 10.1016/j.molcel.2009.01.026. View

18.

Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg A . Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature. 2008; 451(7175):202-6. PMC: 2743558. DOI: 10.1038/nature06468. View

19.

Faghihi M, Modarresi F, Khalil A, Wood D, Sahagan B, Morgan T . Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat Med. 2008; 14(7):723-30. PMC: 2826895. DOI: 10.1038/nm1784. View

20.

Khalil A, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D . Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009; 106(28):11667-72. PMC: 2704857. DOI: 10.1073/pnas.0904715106. View