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Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1.

Creamer TJ, Darby MM, Jamonnak N, Schaughency P, Hao H, Wheelan SJ, Corden JL.

PLoS Genet. 2011 Oct;7(10):e1002329. doi: 10.1371/journal.pgen.1002329. Epub 2011 Oct 20.


Distinct RNA degradation pathways and 3' extensions of yeast non-coding RNA species.

Marquardt S, Hazelbaker DZ, Buratowski S.

Transcription. 2011 May;2(3):145-154.


Unravelling the means to an end: RNA polymerase II transcription termination.

Kuehner JN, Pearson EL, Moore C.

Nat Rev Mol Cell Biol. 2011 May;12(5):283-94. doi: 10.1038/nrm3098. Epub 2011 Apr 13. Review.


The nuclear RNA polymerase II surveillance system targets polymerase III transcripts.

Wlotzka W, Kudla G, Granneman S, Tollervey D.

EMBO J. 2011 May 4;30(9):1790-803. doi: 10.1038/emboj.2011.97. Epub 2011 Apr 1. Erratum in: EMBO J. 2011;30(14):2982.


Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation.

Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan AP, John B, Milos PM.

Cell. 2010 Dec 10;143(6):1018-29. doi: 10.1016/j.cell.2010.11.020.


Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species.

Yassour M, Pfiffner J, Levin JZ, Adiconis X, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A.

Genome Biol. 2010;11(8):R87. doi: 10.1186/gb-2010-11-8-r87. Epub 2010 Aug 26.


MochiView: versatile software for genome browsing and DNA motif analysis.

Homann OR, Johnson AD.

BMC Biol. 2010 Apr 21;8:49. doi: 10.1186/1741-7007-8-49.


Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP.

Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T.

Cell. 2010 Apr 2;141(1):129-41. doi: 10.1016/j.cell.2010.03.009.


Sen1p performs two genetically separable functions in transcription and processing of U5 small nuclear RNA in Saccharomyces cerevisiae.

Finkel JS, Chinchilla K, Ursic D, Culbertson MR.

Genetics. 2010 Jan;184(1):107-18. doi: 10.1534/genetics.109.110031. Epub 2009 Nov 2.


Nuclear RNA surveillance: no sign of substrates tailing off.

Anderson JT, Wang X.

Crit Rev Biochem Mol Biol. 2009 Jan-Feb;44(1):16-24. doi: 10.1080/10409230802640218 . Review.


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.


Widespread bidirectional promoters are the major source of cryptic transcripts in yeast.

Neil H, Malabat C, d'Aubenton-Carafa Y, Xu Z, Steinmetz LM, Jacquier A.

Nature. 2009 Feb 19;457(7232):1038-42. doi: 10.1038/nature07747. Epub 2009 Jan 25.


Bidirectional promoters generate pervasive transcription in yeast.

Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Münster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM.

Nature. 2009 Feb 19;457(7232):1033-7. doi: 10.1038/nature07728. Epub 2009 Jan 25.


Polyadenylation linked to transcription termination directs the processing of snoRNA precursors in yeast.

Grzechnik P, Kufel J.

Mol Cell. 2008 Oct 24;32(2):247-58. doi: 10.1016/j.molcel.2008.10.003.


Futile cycle of transcription initiation and termination modulates the response to nucleotide shortage in S. cerevisiae.

Thiebaut M, Colin J, Neil H, Jacquier A, Séraphin B, Lacroute F, Libri D.

Mol Cell. 2008 Sep 5;31(5):671-82. doi: 10.1016/j.molcel.2008.08.010.


Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice.

Gudipati RK, Villa T, Boulay J, Libri D.

Nat Struct Mol Biol. 2008 Aug;15(8):786-94. doi: 10.1038/nsmb.1460. Epub 2008 Jul 27.


The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain.

Vasiljeva L, Kim M, Mutschler H, Buratowski S, Meinhart A.

Nat Struct Mol Biol. 2008 Aug;15(8):795-804. doi: 10.1038/nsmb.1468. Epub 2008 Jul 27.


Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation.

Kuehner JN, Brow DA.

Mol Cell. 2008 Jul 25;31(2):201-11. doi: 10.1016/j.molcel.2008.05.018.


Properties of an intergenic terminator and start site switch that regulate IMD2 transcription in yeast.

Jenks MH, O'Rourke TW, Reines D.

Mol Cell Biol. 2008 Jun;28(12):3883-93. doi: 10.1128/MCB.00380-08. Epub 2008 Apr 21.


The mRNA encoding the yeast ARE-binding protein Cth2 is generated by a novel 3' processing pathway.

Ciais D, Bohnsack MT, Tollervey D.

Nucleic Acids Res. 2008 May;36(9):3075-84. doi: 10.1093/nar/gkn160. Epub 2008 Apr 8.

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