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Items: 1 to 20 of 57

1.

mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription.

Brannan K, Kim H, Erickson B, Glover-Cutter K, Kim S, Fong N, Kiemele L, Hansen K, Davis R, Lykke-Andersen J, Bentley DL.

Mol Cell. 2012 May 11;46(3):311-24. doi: 10.1016/j.molcel.2012.03.006. Epub 2012 Apr 5.

2.

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA.

Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA, Glass CK, Rosenfeld MG, Fu XD.

Nature. 2011 May 15;474(7351):390-4. doi: 10.1038/nature10006.

3.

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells.

Min IM, Waterfall JJ, Core LJ, Munroe RJ, Schimenti J, Lis JT.

Genes Dev. 2011 Apr 1;25(7):742-54. doi: 10.1101/gad.2005511.

4.

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ.

Nature. 2011 Mar 24;471(7339):480-5. doi: 10.1038/nature09725. Epub 2010 Dec 22.

5.

Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation.

Nechaev S, Adelman K.

Biochim Biophys Acta. 2011 Jan;1809(1):34-45. doi: 10.1016/j.bbagrm.2010.11.001. Epub 2010 Nov 13. Review.

6.

Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation.

Gilchrist DA, Dos Santos G, Fargo DC, Xie B, Gao Y, Li L, Adelman K.

Cell. 2010 Nov 12;143(4):540-51. doi: 10.1016/j.cell.2010.10.004.

7.

Genome-wide translational profiling by ribosome footprinting.

Ingolia NT.

Methods Enzymol. 2010;470:119-42. doi: 10.1016/S0076-6879(10)70006-9. Epub 2010 Mar 1.

PMID:
20946809
8.

Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the Drosophila RNA polymerase II transcription elongation complex.

Missra A, Gilmour DS.

Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11301-6. doi: 10.1073/pnas.1000681107. Epub 2010 Jun 4.

9.

Most "dark matter" transcripts are associated with known genes.

van Bakel H, Nislow C, Blencowe BJ, Hughes TR.

PLoS Biol. 2010 May 18;8(5):e1000371. doi: 10.1371/journal.pbio.1000371.

10.

c-Myc regulates transcriptional pause release.

Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, Sharp PA, Young RA.

Cell. 2010 Apr 30;141(3):432-45. doi: 10.1016/j.cell.2010.03.030.

11.

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.

12.

Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila.

Nechaev S, Fargo DC, dos Santos G, Liu L, Gao Y, Adelman K.

Science. 2010 Jan 15;327(5963):335-8. doi: 10.1126/science.1181421. Epub 2009 Dec 10.

13.

Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling.

Adelman K, Kennedy MA, Nechaev S, Gilchrist DA, Muse GW, Chinenov Y, Rogatsky I.

Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18207-12. doi: 10.1073/pnas.0910177106. Epub 2009 Oct 9.

14.

Synchronous and stochastic patterns of gene activation in the Drosophila embryo.

Boettiger AN, Levine M.

Science. 2009 Jul 24;325(5939):471-3. doi: 10.1126/science.1173976.

15.

Divergent transcription: a new feature of active promoters.

Seila AC, Core LJ, Lis JT, Sharp PA.

Cell Cycle. 2009 Aug 15;8(16):2557-64. Epub 2009 Aug 19. Review.

PMID:
19597342
16.

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
17.

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead B, Trapnell C, Pop M, Salzberg SL.

Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.

18.

RNA Pol II accumulates at promoters of growth genes during developmental arrest.

Baugh LR, Demodena J, Sternberg PW.

Science. 2009 Apr 3;324(5923):92-4. doi: 10.1126/science.1169628. Epub 2009 Feb 26.

19.

Transcription. Gene expression--where to start?

Buratowski S.

Science. 2008 Dec 19;322(5909):1804-5. doi: 10.1126/science.1168805. No abstract available.

20.

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.

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