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Items: 1 to 20 of 54

1.

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions.

Lin MF, Jungreis I, Kellis M.

Bioinformatics. 2011 Jul 1;27(13):i275-82. doi: 10.1093/bioinformatics/btr209.

2.

A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response.

Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M, Attardi LD, Regev A, Lander ES, Jacks T, Rinn JL.

Cell. 2010 Aug 6;142(3):409-19. doi: 10.1016/j.cell.2010.06.040.

3.

Long noncoding RNA as modular scaffold of histone modification complexes.

Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY.

Science. 2010 Aug 6;329(5992):689-93. doi: 10.1126/science.1192002. Epub 2010 Jul 8.

4.

RNase-assisted RNA chromatography.

Michlewski G, Cáceres JF.

RNA. 2010 Aug;16(8):1673-8. doi: 10.1261/rna.2136010. Epub 2010 Jun 22.

5.

Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2.

Kanhere A, Viiri K, Araújo CC, Rasaiyaah J, Bouwman RD, Whyte WA, Pereira CF, Brookes E, Walker K, Bell GW, Pombo A, Fisher AG, Young RA, Jenner RG.

Mol Cell. 2010 Jun 11;38(5):675-88. doi: 10.1016/j.molcel.2010.03.019.

6.

A large fraction of extragenic RNA pol II transcription sites overlap enhancers.

De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, Muller H, Ragoussis J, Wei CL, Natoli G.

PLoS Biol. 2010 May 11;8(5):e1000384. doi: 10.1371/journal.pbio.1000384.

7.

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis.

Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY.

Nature. 2010 Apr 15;464(7291):1071-6. doi: 10.1038/nature08975.

8.

Widespread transcription at neuronal activity-regulated enhancers.

Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S, Markenscoff-Papadimitriou E, Kuhl D, Bito H, Worley PF, Kreiman G, Greenberg ME.

Nature. 2010 May 13;465(7295):182-7. doi: 10.1038/nature09033. Epub 2010 Apr 14.

9.

Regulation of the p53 transcriptional response by structurally diverse core promoters.

Morachis JM, Murawsky CM, Emerson BM.

Genes Dev. 2010 Jan 15;24(2):135-47. doi: 10.1101/gad.1856710. Epub 2009 Dec 29.

10.

Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome.

Lee JT.

Genes Dev. 2009 Aug 15;23(16):1831-42. doi: 10.1101/gad.1811209.

11.

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression.

Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL.

Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11667-72. doi: 10.1073/pnas.0904715106. Epub 2009 Jul 1.

12.

Tiny RNAs associated with transcription start sites in animals.

Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest AR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub CO, Hume DA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y, Mattick JS.

Nat Genet. 2009 May;41(5):572-8. doi: 10.1038/ng.312. Epub 2009 Apr 19. Erratum in: Nat Genet. 2009 Jul;41(7):859.

PMID:
19377478
13.

Genome-wide views of chromatin structure.

Rando OJ, Chang HY.

Annu Rev Biochem. 2009;78:245-71. doi: 10.1146/annurev.biochem.78.071107.134639. Review.

14.

EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data.

Bock C, Halachev K, Büch J, Lengauer T.

Genome Biol. 2009 Feb 10;10(2):R14. doi: 10.1186/gb-2009-10-2-r14.

15.

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.

Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES.

Nature. 2009 Mar 12;458(7235):223-7. doi: 10.1038/nature07672. Epub 2009 Feb 1.

16.

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters.

Core LJ, Waterfall JJ, Lis JT.

Science. 2008 Dec 19;322(5909):1845-8. doi: 10.1126/science.1162228. Epub 2008 Dec 4.

17.

Divergent transcription from active promoters.

Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA.

Science. 2008 Dec 19;322(5909):1849-51. doi: 10.1126/science.1162253. Epub 2008 Dec 4.

18.

Non-coding RNA transcription: turning on neighbours.

Carninci P.

Nat Cell Biol. 2008 Sep;10(9):1023-4. doi: 10.1038/ncb0908-1023.

PMID:
18758492
19.

Antisense transcripts are targets for activating small RNAs.

Schwartz JC, Younger ST, Nguyen NB, Hardy DB, Monia BP, Corey DR, Janowski BA.

Nat Struct Mol Biol. 2008 Aug;15(8):842-8. doi: 10.1038/nsmb.1444. Epub 2008 Jul 6.

20.

Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription.

Wang X, Arai S, Song X, Reichart D, Du K, Pascual G, Tempst P, Rosenfeld MG, Glass CK, Kurokawa R.

Nature. 2008 Jul 3;454(7200):126-30. doi: 10.1038/nature06992. Epub 2008 May 28.

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