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Rapid Amplification of 5' cDNA Ends (5'-RACE).

Sambrook J, Russell DW.

CSH Protoc. 2006 Jun 1;2006(1). pii: pdb.prot3989. doi: 10.1101/pdb.prot3989. No abstract available.


Rapid Amplification of 3' cDNA Ends (3'-RACE).

Sambrook J, Russell DW.

CSH Protoc. 2006 Jun 1;2006(1). pii: pdb.prot3865. doi: 10.1101/pdb.prot3865. No abstract available.


Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.

Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei CL, Ge W, Wang H, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, Fullwood MJ, Cheung E, Liu E, Sung WK, Snyder M, Ruan Y.

Cell. 2012 Jan 20;148(1-2):84-98. doi: 10.1016/j.cell.2011.12.014.


The Hbo1-Brd1/Brpf2 complex is responsible for global acetylation of H3K14 and required for fetal liver erythropoiesis.

Mishima Y, Miyagi S, Saraya A, Negishi M, Endoh M, Endo TA, Toyoda T, Shinga J, Katsumoto T, Chiba T, Yamaguchi N, Kitabayashi I, Koseki H, Iwama A.

Blood. 2011 Sep 1;118(9):2443-53. doi: 10.1182/blood-2011-01-331892. Epub 2011 Jul 13.


Structural and histone binding ability characterizations of human PWWP domains.

Wu H, Zeng H, Lam R, Tempel W, Amaya MF, Xu C, Dombrovski L, Qiu W, Wang Y, Min J.

PLoS One. 2011;6(6):e18919. doi: 10.1371/journal.pone.0018919. Epub 2011 Jun 20.


Extensive relationship between antisense transcription and alternative splicing in the human genome.

Morrissy AS, Griffith M, Marra MA.

Genome Res. 2011 Aug;21(8):1203-12. doi: 10.1101/gr.113431.110. Epub 2011 Jun 30.


Analysis of the human endogenous coregulator complexome.

Malovannaya A, Lanz RB, Jung SY, Bulynko Y, Le NT, Chan DW, Ding C, Shi Y, Yucer N, Krenciute G, Kim BJ, Li C, Chen R, Li W, Wang Y, O'Malley BW, Qin J.

Cell. 2011 May 27;145(5):787-99. doi: 10.1016/j.cell.2011.05.006.


Pre-mRNA splicing: where and when in the nucleus.

Han J, Xiong J, Wang D, Fu XD.

Trends Cell Biol. 2011 Jun;21(6):336-43. doi: 10.1016/j.tcb.2011.03.003. Epub 2011 Apr 21. Review.


A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression.

Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY.

Nature. 2011 Apr 7;472(7341):120-4. doi: 10.1038/nature09819. Epub 2011 Mar 20.


Enhancer function: new insights into the regulation of tissue-specific gene expression.

Ong CT, Corces VG.

Nat Rev Genet. 2011 Apr;12(4):283-93. doi: 10.1038/nrg2957. Epub 2011 Mar 1. Review.


FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.

Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D.

Nat Methods. 2010 Dec;7(12):995-1001. doi: 10.1038/nmeth.1529. Epub 2010 Nov 7.


Long noncoding RNAs with enhancer-like function in human cells.

├śrom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R.

Cell. 2010 Oct 1;143(1):46-58. doi: 10.1016/j.cell.2010.09.001.


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.


Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L.

Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2.


Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.

Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A.

Nat Biotechnol. 2010 May;28(5):503-10. doi: 10.1038/nbt.1633. Epub 2010 May 2. Erratum in: Nat Biotechnol. 2010 Jul;28(7):756.


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.


Xenopus RCOR2 (REST corepressor 2) interacts with ZMYND8, which is involved in neural differentiation.

Zeng W, Kong Q, Li C, Mao B.

Biochem Biophys Res Commun. 2010 Apr 16;394(4):1024-9. doi: 10.1016/j.bbrc.2010.03.115. Epub 2010 Mar 21.


Identification of a functional network of human epigenetic silencing factors.

Poleshko A, Einarson MB, Shalginskikh N, Zhang R, Adams PD, Skalka AM, Katz RA.

J Biol Chem. 2010 Jan 1;285(1):422-33. doi: 10.1074/jbc.M109.064667. Epub 2009 Oct 30.


"Cotranscriptionality": the transcription elongation complex as a nexus for nuclear transactions.

Perales R, Bentley D.

Mol Cell. 2009 Oct 23;36(2):178-91. doi: 10.1016/j.molcel.2009.09.018. Review.


Human DNA methylomes at base resolution show widespread epigenomic differences.

Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR.

Nature. 2009 Nov 19;462(7271):315-22. doi: 10.1038/nature08514. Epub 2009 Oct 14.

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