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Widespread Backtracking by RNA Pol II Is a Major Effector of Gene Activation, 5' Pause Release, Termination, and Transcription Elongation Rate.

Sheridan RM, Fong N, D'Alessandro A, Bentley DL.

Mol Cell. 2019 Jan 3;73(1):107-118.e4. doi: 10.1016/j.molcel.2018.10.031. Epub 2018 Nov 29.


Dynamic turnover of paused Pol II complexes at human promoters.

Erickson B, Sheridan RM, Cortazar M, Bentley DL.

Genes Dev. 2018 Sep 1;32(17-18):1215-1225. doi: 10.1101/gad.316810.118. Epub 2018 Aug 27.


Corrigendum: Transcription elongation rate affects nascent histone pre-mRNA folding and 3' end processing.

Saldi T, Fong N, Bentley DL.

Genes Dev. 2018 Apr 1;32(7-8):592. doi: 10.1101/gad.314948.118. No abstract available.


Transcription elongation rate affects nascent histone pre-mRNA folding and 3' end processing.

Saldi T, Fong N, Bentley DL.

Genes Dev. 2018 Feb 1;32(3-4):297-308. doi: 10.1101/gad.310896.117. Epub 2018 Feb 26. Erratum in: Genes Dev. 2018 Apr 1;32(7-8):592.


Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications.

Ebmeier CC, Erickson B, Allen BL, Allen MA, Kim H, Fong N, Jacobsen JR, Liang K, Shilatifard A, Dowell RD, Old WM, Bentley DL, Taatjes DJ.

Cell Rep. 2017 Aug 1;20(5):1173-1186. doi: 10.1016/j.celrep.2017.07.021.


Breast Cancer Suppression by Progesterone Receptors Is Mediated by Their Modulation of Estrogen Receptors and RNA Polymerase III.

Finlay-Schultz J, Gillen AE, Brechbuhl HM, Ivie JJ, Matthews SB, Jacobsen BM, Bentley DL, Kabos P, Sartorius CA.

Cancer Res. 2017 Sep 15;77(18):4934-4946. doi: 10.1158/0008-5472.CAN-16-3541. Epub 2017 Jul 20.


RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction.

Fong N, Saldi T, Sheridan RM, Cortazar MA, Bentley DL.

Mol Cell. 2017 May 18;66(4):546-557.e3. doi: 10.1016/j.molcel.2017.04.016. Epub 2017 May 11.


Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing.

Saldi T, Cortazar MA, Sheridan RM, Bentley DL.

J Mol Biol. 2016 Jun 19;428(12):2623-2635. doi: 10.1016/j.jmb.2016.04.017. Epub 2016 Apr 20. Review.


Selectable one-step PCR-mediated integration of a degron for rapid depletion of endogenous human proteins.

Sheridan RM, Bentley DL.

Biotechniques. 2016 Feb 1;60(2):69-74. doi: 10.2144/000114378. eCollection 2016 Feb.


Coordination of RNA Polymerase II Pausing and 3' End Processing Factor Recruitment with Alternative Polyadenylation.

Fusby B, Kim S, Erickson B, Kim H, Peterson ML, Bentley DL.

Mol Cell Biol. 2015 Nov 2;36(2):295-303. doi: 10.1128/MCB.00898-15. Print 2016 Jan 15.


Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition.

Fong N, Brannan K, Erickson B, Kim H, Cortazar MA, Sheridan RM, Nguyen T, Karp S, Bentley DL.

Mol Cell. 2015 Oct 15;60(2):256-67. doi: 10.1016/j.molcel.2015.09.026.


The union of transcription and mRNA processing: 20 years of coupling.

Bentley DL.

RNA. 2015 Apr;21(4):569-70. doi: 10.1261/rna.050740.115. No abstract available.


Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate.

Fong N, Kim H, Zhou Y, Ji X, Qiu J, Saldi T, Diener K, Jones K, Fu XD, Bentley DL.

Genes Dev. 2014 Dec 1;28(23):2663-76. doi: 10.1101/gad.252106.114.


Coupling mRNA processing with transcription in time and space.

Bentley DL.

Nat Rev Genet. 2014 Mar;15(3):163-75. doi: 10.1038/nrg3662. Epub 2014 Feb 11. Review.


The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD fingers.

Klein BJ, Piao L, Xi Y, Rincon-Arano H, Rothbart SB, Peng D, Wen H, Larson C, Zhang X, Zheng X, Cortazar MA, Peña PV, Mangan A, Bentley DL, Strahl BD, Groudine M, Li W, Shi X, Kutateladze TG.

Cell Rep. 2014 Jan 30;6(2):325-35. doi: 10.1016/j.celrep.2013.12.021. Epub 2014 Jan 9.


In vivo time-serial multi-modality optical imaging in a mouse model of ovarian tumorigenesis.

Watson JM, Marion SL, Rice PF, Bentley DL, Besselsen DG, Utzinger U, Hoyer PB, Barton JK.

Cancer Biol Ther. 2014 Jan;15(1):42-60. doi: 10.4161/cbt.26605. Epub 2013 Oct 3.


Cyclin-dependent kinase control of the initiation-to-elongation switch of RNA polymerase II.

Larochelle S, Amat R, Glover-Cutter K, Sansó M, Zhang C, Allen JJ, Shokat KM, Bentley DL, Fisher RP.

Nat Struct Mol Biol. 2012 Nov;19(11):1108-15. doi: 10.1038/nsmb.2399. Epub 2012 Oct 14.


Control of Transcriptional Elongation by RNA Polymerase II: A Retrospective.

Brannan K, Bentley DL.

Genet Res Int. 2012;2012:170173. doi: 10.1155/2012/170173. Epub 2012 Jan 29.


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.


The export factor Yra1 modulates mRNA 3' end processing.

Johnson SA, Kim H, Erickson B, Bentley DL.

Nat Struct Mol Biol. 2011 Sep 25;18(10):1164-71. doi: 10.1038/nsmb.2126.


Pre-mRNA splicing is a determinant of histone H3K36 methylation.

Kim S, Kim H, Fong N, Erickson B, Bentley DL.

Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13564-9. doi: 10.1073/pnas.1109475108. Epub 2011 Aug 1.


Gene-specific RNA polymerase II phosphorylation and the CTD code.

Kim H, Erickson B, Luo W, Seward D, Graber JH, Pollock DD, Megee PC, Bentley DL.

Nat Struct Mol Biol. 2010 Oct;17(10):1279-86. doi: 10.1038/nsmb.1913. Epub 2010 Sep 12.


Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing.

Fong N, Ohman M, Bentley DL.

Nat Struct Mol Biol. 2009 Sep;16(9):916-22. doi: 10.1038/nsmb.1652. Epub 2009 Aug 23.


TFIIH-associated Cdk7 kinase functions in phosphorylation of C-terminal domain Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase II.

Glover-Cutter K, Larochelle S, Erickson B, Zhang C, Shokat K, Fisher RP, Bentley DL.

Mol Cell Biol. 2009 Oct;29(20):5455-64. doi: 10.1128/MCB.00637-09. Epub 2009 Aug 10.


Cotranscriptional recruitment of the mRNA export factor Yra1 by direct interaction with the 3' end processing factor Pcf11.

Johnson SA, Cubberley G, Bentley DL.

Mol Cell. 2009 Jan 30;33(2):215-26. doi: 10.1016/j.molcel.2008.12.007. Epub 2008 Dec 24.


RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes.

Glover-Cutter K, Kim S, Espinosa J, Bentley DL.

Nat Struct Mol Biol. 2008 Jan;15(1):71-8. Epub 2007 Dec 23.


The C-terminal domain of RNA Pol II helps ensure that editing precedes splicing of the GluR-B transcript.

Ryman K, Fong N, Bratt E, Bentley DL, Ohman M.

RNA. 2007 Jul;13(7):1071-8. Epub 2007 May 24.


Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins.

Seward DJ, Cubberley G, Kim S, Schonewald M, Zhang L, Tripet B, Bentley DL.

Nat Struct Mol Biol. 2007 Mar;14(3):240-2. Epub 2007 Feb 18.


Phase-variable expression of a family of glycoproteins imparts a dynamic surface to a symbiont in its human intestinal ecosystem.

Fletcher CM, Coyne MJ, Bentley DL, Villa OF, Comstock LE.

Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2413-8. Epub 2007 Feb 6.


Splicing speckles are not reservoirs of RNA polymerase II, but contain an inactive form, phosphorylated on serine2 residues of the C-terminal domain.

Xie SQ, Martin S, Guillot PV, Bentley DL, Pombo A.

Mol Biol Cell. 2006 Apr;17(4):1723-33. Epub 2006 Feb 8.


RNA editing and alternative splicing: the importance of co-transcriptional coordination.

Laurencikiene J, Källman AM, Fong N, Bentley DL, Ohman M.

EMBO Rep. 2006 Mar;7(3):303-7. Epub 2006 Jan 27.


Ribozyme cleavage reveals connections between mRNA release from the site of transcription and pre-mRNA processing.

Bird G, Fong N, Gatlin JC, Farabaugh S, Bentley DL.

Mol Cell. 2005 Dec 9;20(5):747-58.


Altered nucleosome occupancy and histone H3K4 methylation in response to 'transcriptional stress'.

Zhang L, Schroeder S, Fong N, Bentley DL.

EMBO J. 2005 Jul 6;24(13):2379-90. Epub 2005 Jun 9.


Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors.

Bentley DL.

Curr Opin Cell Biol. 2005 Jun;17(3):251-6. Review.


The link between mRNA processing and transcription: communication works both ways.

Zorio DA, Bentley DL.

Exp Cell Res. 2004 May 15;296(1):91-7. Review.


The C-terminal domain of pol II and a DRB-sensitive kinase are required for 3' processing of U2 snRNA.

Medlin JE, Uguen P, Taylor A, Bentley DL, Murphy S.

EMBO J. 2003 Feb 17;22(4):925-34.


Functional interaction of yeast pre-mRNA 3' end processing factors with RNA polymerase II.

Licatalosi DD, Geiger G, Minet M, Schroeder S, Cilli K, McNeil JB, Bentley DL.

Mol Cell. 2002 May;9(5):1101-11.


Subcellular localization of NAD(P)H:quinone oxidoreductase 1 in human cancer cells.

Winski SL, Koutalos Y, Bentley DL, Ross D.

Cancer Res. 2002 Mar 1;62(5):1420-4.


Assessment of white matter injury following prolonged focal cerebral ischaemia in the rat.

Irving EA, Bentley DL, Parsons AA.

Acta Neuropathol. 2001 Dec;102(6):627-35.


Transcription elongation: the 'Foggy' is liftingellipsis.

Zorio DA, Bentley DL.

Curr Biol. 2001 Feb 20;11(4):R144-6. Review.


MCM proteins are associated with RNA polymerase II holoenzyme.

Yankulov K, Todorov I, Romanowski P, Licatalosi D, Cilli K, McCracken S, Laskey R, Bentley DL.

Mol Cell Biol. 1999 Sep;19(9):6154-63.


Optimization of capillary chromatography ion trap-mass spectrometry for identification of gel-separated proteins.

Courchesne PL, Jones MD, Robinson JH, Spahr CS, McCracken S, Bentley DL, Luethy R, Patterson SD.

Electrophoresis. 1998 May;19(6):956-67.


5'-Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II.

McCracken S, Fong N, Rosonina E, Yankulov K, Brothers G, Siderovski D, Hessel A, Foster S, Shuman S, Bentley DL.

Genes Dev. 1997 Dec 15;11(24):3306-18.


Regulation of CDK7 substrate specificity by MAT1 and TFIIH.

Yankulov KY, Bentley DL.

EMBO J. 1997 Apr 1;16(7):1638-46.


Protective monoclonal antibody defines a circumsporozoite-like glycoprotein exoantigen of Cryptosporidium parvum sporozoites and merozoites.

Riggs MW, Stone AL, Yount PA, Langer RC, Arrowood MJ, Bentley DL.

J Immunol. 1997 Feb 15;158(4):1787-95.


The C-terminal domain of RNA polymerase II couples mRNA processing to transcription.

McCracken S, Fong N, Yankulov K, Ballantyne S, Pan G, Greenblatt J, Patterson SD, Wickens M, Bentley DL.

Nature. 1997 Jan 23;385(6614):357-61.


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