Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
Keywords
Last Name
Institution

David L Bentley

TitleProfessor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-BioChem&Molecular Genetics
Phone303/724-3238

    Collapse Research 
    Collapse research activities and funding
    R35GM144336     (BENTLEY, DAVID L)Feb 1, 2022 - Jan 31, 2027
    NIH
    Coupling of transcription elongation and termination with pre-mRNA processing
    Role: Principal Investigator
    R01HD100935     (BENTLEY, DAVID LEONARD)Sep 20, 2019 - Jun 30, 2024
    NIH
    Trisomy 21 and RNA polymerase II function
    Role: Principal Investigator
    R35GM118051     (BENTLEY, DAVID LEONARD)May 1, 2016 - Apr 30, 2021
    NIH
    Coupling of transcription with nascent pre-mRNA metabolism
    Role: Principal Investigator
    R01CA170859     (BENTLEY, DAVID LEONARD)Aug 1, 2012 - May 31, 2016
    NIH
    Mis-regulation of mRNA poly (A) site selection in cancer cells (PQ11)
    Role: Principal Investigator
    R01GM063873     (BENTLEY, DAVID LEONARD)Jul 1, 2001 - Feb 28, 2017
    NIH
    Elongation and termination of transcripts by RNA pol II
    Role: Principal Investigator
    R01GM058613     (BENTLEY, DAVID LEONARD)Jan 1, 1999 - Dec 31, 2015
    NIH
    Coupling of transcription with pre-mRNA metabolism
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Cozzolino K, Sanford L, Hunter S, Molison K, Erickson B, Jones T, Courvan MCS, Ajit D, Galbraith MD, Espinosa JM, Bentley DL, Allen MA, Dowell RD, Taatjes DJ. Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome. bioRxiv. 2024 May 28. PMID: 37461585.
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    2. Cort?zar MA, Fong N, Bentley DL. Genome-wide Mapping of 5'-monophosphorylated Ends of Mammalian Nascent RNA Transcripts. Bio Protoc. 2023 Sep 20; 13(18):e4828. PMID: 37753464.
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    3. Shenasa H, Bentley DL. Pre-mRNA splicing and its cotranscriptional connections. Trends Genet. 2023 09; 39(9):672-685. PMID: 37236814.
      View in: PubMed
    4. Geisberg JV, Moqtaderi Z, Fong N, Erickson B, Bentley DL, Struhl K. Nucleotide-level linkage of transcriptional elongation and polyadenylation. Elife. 2022 11 24; 11. PMID: 36421680.
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    5. Fong N, Sheridan RM, Ramachandran S, Bentley DL. The pausing zone and control of RNA polymerase II elongation by Spt5: Implications for the pause-release model. Mol Cell. 2022 10 06; 82(19):3632-3645.e4. PMID: 36206739.
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    6. Cortazar MA, Erickson B, Fong N, Pradhan SJ, Ntini E, Bentley DL. Xrn2 substrate mapping identifies torpedo loading sites and extensive premature termination of RNA pol II transcription. Genes Dev. 2022 10 01; 36(19-20):1062-1078. PMID: 36396340.
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    7. Goering R, Engel KL, Gillen AE, Fong N, Bentley DL, Taliaferro JM. LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival. BMC Genomics. 2021 Jun 26; 22(1):476. PMID: 34174817.
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    8. Saldi T, Riemondy K, Erickson B, Bentley DL. Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing. Mol Cell. 2021 04 15; 81(8):1789-1801.e5. PMID: 33631106.
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    9. Rimel JK, Poss ZC, Erickson B, Maas ZL, Ebmeier CC, Johnson JL, Decker TM, Yaron TM, Bradley MJ, Hamman KB, Hu S, Malojcic G, Marineau JJ, White PW, Brault M, Tao L, DeRoy P, Clavette C, Nayak S, Damon LJ, Kaltheuner IH, Bunch H, Cantley LC, Geyer M, Iwasa J, Dowell RD, Bentley DL, Old WM, Taatjes DJ. Selective inhibition of CDK7 reveals high-confidence targets and new models for TFIIH function in transcription. Genes Dev. 2020 11 01; 34(21-22):1452-1473. PMID: 33060135.
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    10. Cortazar MA, Sheridan RM, Erickson B, Fong N, Glover-Cutter K, Brannan K, Bentley DL. Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a "Sitting Duck Torpedo" Mechanism. Mol Cell. 2019 12 19; 76(6):896-908.e4. PMID: 31677974.
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    11. Sheridan RM, Fong N, D'Alessandro A, Bentley DL. Widespread Backtracking by RNA Pol II Is a Major Effector of Gene Activation, 5' Pause Release, Termination, and Transcription Elongation Rate. Mol Cell. 2019 01 03; 73(1):107-118.e4. PMID: 30503775.
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    12. Erickson B, Sheridan RM, Cortazar M, Bentley DL. Dynamic turnover of paused Pol II complexes at human promoters. Genes Dev. 2018 09 01; 32(17-18):1215-1225. PMID: 30150253.
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    13. Saldi T, Fong N, Bentley DL. Corrigendum: Transcription elongation rate affects nascent histone pre-mRNA folding and 3' end processing. Genes Dev. 2018 04 01; 32(7-8):592. PMID: 29692357.
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    14. Saldi T, Fong N, Bentley DL. Transcription elongation rate affects nascent histone pre-mRNA folding and 3' end processing. Genes Dev. 2018 02 01; 32(3-4):297-308. PMID: 29483154.
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    15. 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. Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications. Cell Rep. 2017 08 01; 20(5):1173-1186. PMID: 28768201.
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    16. Finlay-Schultz J, Gillen AE, Brechbuhl HM, Ivie JJ, Matthews SB, Jacobsen BM, Bentley DL, Kabos P, Sartorius CA. Breast Cancer Suppression by Progesterone Receptors Is Mediated by Their Modulation of Estrogen Receptors and RNA Polymerase III. Cancer Res. 2017 09 15; 77(18):4934-4946. PMID: 28729413.
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    17. Fong N, Saldi T, Sheridan RM, Cortazar MA, Bentley DL. RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction. Mol Cell. 2017 May 18; 66(4):546-557.e3. PMID: 28506463.
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    18. Kerherve G, Regoutz A, Bentley D, Hood C, Feeley K, Knight S, Robson A, Turner C, Singh N, Pontefract J, ?hlund J, Kahk JM, Villar-Garcia IJ, Payne DJ. Laboratory-based high pressure X-ray photoelectron spectroscopy: A novel and flexible reaction cell approach. Rev Sci Instrum. 2017 Mar; 88(3):033102. PMID: 28372401.
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    19. Saldi T, Cortazar MA, Sheridan RM, Bentley DL. Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing. J Mol Biol. 2016 06 19; 428(12):2623-2635. PMID: 27107644.
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    20. Sheridan RM, Bentley DL. Selectable one-step PCR-mediated integration of a degron for rapid depletion of endogenous human proteins. Biotechniques. 2016 Feb; 60(2):69-74. PMID: 26842351.
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    21. Fusby B, Kim S, Erickson B, Kim H, Peterson ML, Bentley DL. Coordination of RNA Polymerase II Pausing and 3' End Processing Factor Recruitment with Alternative Polyadenylation. Mol Cell Biol. 2016 01 15; 36(2):295-303. PMID: 26527620.
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    22. Fong N, Brannan K, Erickson B, Kim H, Cortazar MA, Sheridan RM, Nguyen T, Karp S, Bentley DL. Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition. Mol Cell. 2015 Oct 15; 60(2):256-67. PMID: 26474067.
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    23. Bentley DL. The union of transcription and mRNA processing: 20 years of coupling. RNA. 2015 Apr; 21(4):569-70. PMID: 25780142.
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    24. Fong N, Kim H, Zhou Y, Ji X, Qiu J, Saldi T, Diener K, Jones K, Fu XD, Bentley DL. Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes Dev. 2014 Dec 01; 28(23):2663-76. PMID: 25452276.
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    25. Bentley DL. Coupling mRNA processing with transcription in time and space. Nat Rev Genet. 2014 03; 15(3):163-75. PMID: 24514444.
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    26. Klein BJ, Piao L, Xi Y, Rincon-Arano H, Rothbart SB, Peng D, Wen H, Larson C, Zhang X, Zheng X, Cortazar MA, Pe?a PV, Mangan A, Bentley DL, Strahl BD, Groudine M, Li W, Shi X, Kutateladze TG. The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD fingers. Cell Rep. 2014 Jan 30; 6(2):325-35. PMID: 24412361.
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    27. Leonard B, Hart SN, Burns MB, Carpenter MA, Temiz NA, Rathore A, Vogel RI, Nikas JB, Law EK, Brown WL, Li Y, Zhang Y, Maurer MJ, Oberg AL, Cunningham JM, Shridhar V, Bell DA, April C, Bentley D, Bibikova M, Cheetham RK, Fan JB, Grocock R, Humphray S, Kingsbury Z, Peden J, Chien J, Swisher EM, Hartmann LC, Kalli KR, Goode EL, Sicotte H, Kaufmann SH, Harris RS. APOBEC3B upregulation and genomic mutation patterns in serous ovarian carcinoma. Cancer Res. 2013 Dec 15; 73(24):7222-31. PMID: 24154874.
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    28. Watson JM, Marion SL, Rice PF, Bentley DL, Besselsen DG, Utzinger U, Hoyer PB, Barton JK. In vivo time-serial multi-modality optical imaging in a mouse model of ovarian tumorigenesis. Cancer Biol Ther. 2014 Jan; 15(1):42-60. PMID: 24145178.
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    29. Perales R, Erickson B, Zhang L, Kim H, Valiquett E, Bentley D. Gene promoters dictate histone occupancy within genes. EMBO J. 2013 Oct 02; 32(19):2645-56. PMID: 24013117.
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    30. Murtaza M, Dawson SJ, Tsui DW, Gale D, Forshew T, Piskorz AM, Parkinson C, Chin SF, Kingsbury Z, Wong AS, Marass F, Humphray S, Hadfield J, Bentley D, Chin TM, Brenton JD, Caldas C, Rosenfeld N. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature. 2013 May 02; 497(7447):108-12. PMID: 23563269.
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    31. Larochelle S, Amat R, Glover-Cutter K, Sans? M, Zhang C, Allen JJ, Shokat KM, Bentley DL, Fisher RP. Cyclin-dependent kinase control of the initiation-to-elongation switch of RNA polymerase II. Nat Struct Mol Biol. 2012 Nov; 19(11):1108-15. PMID: 23064645.
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    32. Brannan K, Kim H, Erickson B, Glover-Cutter K, Kim S, Fong N, Kiemele L, Hansen K, Davis R, Lykke-Andersen J, Bentley DL. mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. Mol Cell. 2012 May 11; 46(3):311-24. PMID: 22483619.
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    33. Brannan K, Bentley DL. Control of Transcriptional Elongation by RNA Polymerase II: A Retrospective. Genet Res Int. 2012; 2012:170173. PMID: 22567377.
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    34. Johnson SA, Kim H, Erickson B, Bentley DL. The export factor Yra1 modulates mRNA 3' end processing. Nat Struct Mol Biol. 2011 Sep 25; 18(10):1164-71. PMID: 21947206.
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    35. Kim S, Kim H, Fong N, Erickson B, Bentley DL. Pre-mRNA splicing is a determinant of histone H3K36 methylation. Proc Natl Acad Sci U S A. 2011 Aug 16; 108(33):13564-9. PMID: 21807997.
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    36. Perales R, Zhang L, Bentley D. Histone occupancy in vivo at the 601 nucleosome binding element is determined by transcriptional history. Mol Cell Biol. 2011 Aug; 31(16):3485-96. PMID: 21690290.
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    37. Kim H, Erickson B, Luo W, Seward D, Graber JH, Pollock DD, Megee PC, Bentley DL. Gene-specific RNA polymerase II phosphorylation and the CTD code. Nat Struct Mol Biol. 2010 Oct; 17(10):1279-86. PMID: 20835241.
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    38. Waddell T, Gollins S, Soe W, Valle J, Allen J, Bentley D, Morris J, Lloyd A, Swindell R, Taylor MB, Saunders MP. Phase II study of short-course capecitabine plus oxaliplatin (XELOX) followed by maintenance capecitabine in advanced colorectal cancer: XelQuali study. Cancer Chemother Pharmacol. 2011 May; 67(5):1111-7. PMID: 20676676.
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    39. Perales R, Bentley D. "Cotranscriptionality": the transcription elongation complex as a nexus for nuclear transactions. Mol Cell. 2009 Oct 23; 36(2):178-91. PMID: 19854129.
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    40. Fong N, Ohman M, Bentley DL. Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing. Nat Struct Mol Biol. 2009 Sep; 16(9):916-22. PMID: 19701200.
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    41. Glover-Cutter K, Larochelle S, Erickson B, Zhang C, Shokat K, Fisher RP, Bentley DL. TFIIH-associated Cdk7 kinase functions in phosphorylation of C-terminal domain Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase II. Mol Cell Biol. 2009 Oct; 29(20):5455-64. PMID: 19667075.
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    42. Mu?oz MJ, P?rez Santangelo MS, Paronetto MP, de la Mata M, Pelisch F, Boireau S, Glover-Cutter K, Ben-Dov C, Blaustein M, Lozano JJ, Bird G, Bentley D, Bertrand E, Kornblihtt AR. DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation. Cell. 2009 May 15; 137(4):708-20. PMID: 19450518.
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    43. Johnson SA, Cubberley G, Bentley DL. Cotranscriptional recruitment of the mRNA export factor Yra1 by direct interaction with the 3' end processing factor Pcf11. Mol Cell. 2009 Jan 30; 33(2):215-26. PMID: 19110458.
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    44. Glover-Cutter K, Kim S, Espinosa J, Bentley DL. RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nat Struct Mol Biol. 2008 Jan; 15(1):71-8. PMID: 18157150.
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    45. Ryman K, Fong N, Bratt E, Bentley DL, Ohman M. The C-terminal domain of RNA Pol II helps ensure that editing precedes splicing of the GluR-B transcript. RNA. 2007 Jul; 13(7):1071-8. PMID: 17525170.
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    46. Seward DJ, Cubberley G, Kim S, Schonewald M, Zhang L, Tripet B, Bentley DL. Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins. Nat Struct Mol Biol. 2007 Mar; 14(3):240-2. PMID: 17310255.
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    47. Fletcher CM, Coyne MJ, Bentley DL, Villa OF, Comstock LE. Phase-variable expression of a family of glycoproteins imparts a dynamic surface to a symbiont in its human intestinal ecosystem. Proc Natl Acad Sci U S A. 2007 Feb 13; 104(7):2413-8. PMID: 17284602.
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    48. Tassone F, Beilina A, Carosi C, Albertosi S, Bagni C, Li L, Glover K, Bentley D, Hagerman PJ. Elevated FMR1 mRNA in premutation carriers is due to increased transcription. RNA. 2007 Apr; 13(4):555-62. PMID: 17283214.
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    49. Luo W, Johnson AW, Bentley DL. The role of Rat1 in coupling mRNA 3'-end processing to transcription termination: implications for a unified allosteric-torpedo model. Genes Dev. 2006 Apr 15; 20(8):954-65. PMID: 16598041.
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    50. Xie SQ, Martin S, Guillot PV, Bentley DL, Pombo A. Splicing speckles are not reservoirs of RNA polymerase II, but contain an inactive form, phosphorylated on serine2 residues of the C-terminal domain. Mol Biol Cell. 2006 Apr; 17(4):1723-33. PMID: 16467386.
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    51. Laurencikiene J, K?llman AM, Fong N, Bentley DL, Ohman M. RNA editing and alternative splicing: the importance of co-transcriptional coordination. EMBO Rep. 2006 Mar; 7(3):303-7. PMID: 16440002.
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    52. Bird G, Fong N, Gatlin JC, Farabaugh S, Bentley DL. Ribozyme cleavage reveals connections between mRNA release from the site of transcription and pre-mRNA processing. Mol Cell. 2005 Dec 09; 20(5):747-58. PMID: 16337598.
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    53. Zhang L, Schroeder S, Fong N, Bentley DL. Altered nucleosome occupancy and histone H3K4 methylation in response to 'transcriptional stress'. EMBO J. 2005 Jul 06; 24(13):2379-90. PMID: 15944735.
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    54. Bentley DL. Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors. Curr Opin Cell Biol. 2005 Jun; 17(3):251-6. PMID: 15901493.
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    55. Luo W, Bentley D. A ribonucleolytic rat torpedoes RNA polymerase II. Cell. 2004 Dec 29; 119(7):911-4. PMID: 15620350.
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    56. Bird G, Zorio DA, Bentley DL. RNA polymerase II carboxy-terminal domain phosphorylation is required for cotranscriptional pre-mRNA splicing and 3'-end formation. Mol Cell Biol. 2004 Oct; 24(20):8963-9. PMID: 15456870.
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    57. Deloukas P, Earthrowl ME, Grafham DV, Rubenfield M, French L, Steward CA, Sims SK, Jones MC, Searle S, Scott C, Howe K, Hunt SE, Andrews TD, Gilbert JG, Swarbreck D, Ashurst JL, Taylor A, Battles J, Bird CP, Ainscough R, Almeida JP, Ashwell RI, Ambrose KD, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Bates K, Beasley H, Bray-Allen S, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Cahill P, Camire D, Carter NP, Chapman JC, Clark SY, Clarke G, Clee CM, Clegg S, Corby N, Coulson A, Dhami P, Dutta I, Dunn M, Faulkner L, Frankish A, Frankland JA, Garner P, Garnett J, Gribble S, Griffiths C, Grocock R, Gustafson E, Hammond S, Harley JL, Hart E, Heath PD, Ho TP, Hopkins B, Horne J, Howden PJ, Huckle E, Hynds C, Johnson C, Johnson D, Kana A, Kay M, Kimberley AM, Kershaw JK, Kokkinaki M, Laird GK, Lawlor S, Lee HM, Leongamornlert DA, Laird G, Lloyd C, Lloyd DM, Loveland J, Lovell J, McLaren S, McLay KE, McMurray A, Mashreghi-Mohammadi M, Matthews L, Milne S, Nickerson T, Nguyen M, Overton-Larty E, Palmer SA, Pearce AV, Peck AI, Pelan S, Phillimore B, Porter K, Rice CM, Rogosin A, Ross MT, Sarafidou T, Sehra HK, Shownkeen R, Skuce CD, Smith M, Standring L, Sycamore N, Tester J, Thorpe A, Torcasso W, Tracey A, Tromans A, Tsolas J, Wall M, Walsh J, Wang H, Weinstock K, West AP, Willey DL, Whitehead SL, Wilming L, Wray PW, Young L, Chen Y, Lovering RC, Moschonas NK, Siebert R, Fechtel K, Bentley D, Durbin R, Hubbard T, Doucette-Stamm L, Beck S, Smith DR, Rogers J. The DNA sequence and comparative analysis of human chromosome 10. Nature. 2004 May 27; 429(6990):375-81. PMID: 15164054.
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    58. Zorio DA, Bentley DL. The link between mRNA processing and transcription: communication works both ways. Exp Cell Res. 2004 May 15; 296(1):91-7. PMID: 15120999.
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    59. Schroeder SC, Zorio DA, Schwer B, Shuman S, Bentley D. A function of yeast mRNA cap methyltransferase, Abd1, in transcription by RNA polymerase II. Mol Cell. 2004 Feb 13; 13(3):377-87. PMID: 14967145.
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    60. Hughes-Davies L, Huntsman D, Ruas M, Fuks F, Bye J, Chin SF, Milner J, Brown LA, Hsu F, Gilks B, Nielsen T, Schulzer M, Chia S, Ragaz J, Cahn A, Linger L, Ozdag H, Cattaneo E, Jordanova ES, Schuuring E, Yu DS, Venkitaraman A, Ponder B, Doherty A, Aparicio S, Bentley D, Theillet C, Ponting CP, Caldas C, Kouzarides T. EMSY links the BRCA2 pathway to sporadic breast and ovarian cancer. Cell. 2003 Nov 26; 115(5):523-35. PMID: 14651845.
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    61. Fong N, Bird G, Vigneron M, Bentley DL. A 10 residue motif at the C-terminus of the RNA pol II CTD is required for transcription, splicing and 3' end processing. EMBO J. 2003 Aug 15; 22(16):4274-82. PMID: 12912924.
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    62. de la Mata M, Alonso CR, Kadener S, Fededa JP, Blaustein M, Pelisch F, Cramer P, Bentley D, Kornblihtt AR. A slow RNA polymerase II affects alternative splicing in vivo. Mol Cell. 2003 Aug; 12(2):525-32. PMID: 14536091.
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    63. Medlin JE, Uguen P, Taylor A, Bentley DL, Murphy S. The C-terminal domain of pol II and a DRB-sensitive kinase are required for 3' processing of U2 snRNA. EMBO J. 2003 Feb 17; 22(4):925-34. PMID: 12574128.
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    64. Nogues G, Kadener S, Cramer P, Bentley D, Kornblihtt AR. Transcriptional activators differ in their abilities to control alternative splicing. J Biol Chem. 2002 Nov 08; 277(45):43110-4. PMID: 12221105.
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    65. Winski SL, Koutalos Y, Bentley DL, Ross D. Subcellular localization of NAD(P)H:quinone oxidoreductase 1 in human cancer cells. Cancer Res. 2002 Mar 01; 62(5):1420-4. PMID: 11888914.
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    66. Tench C, Bentley D, Vleck V, McCurdie I, White P, D'Cruz D. Aerobic fitness, fatigue, and physical disability in systemic lupus erythematosus. J Rheumatol. 2002 Mar; 29(3):474-81. PMID: 11908559.
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    67. Fong N, Bentley DL. Capping, splicing, and 3' processing are independently stimulated by RNA polymerase II: different functions for different segments of the CTD. Genes Dev. 2001 Jul 15; 15(14):1783-95. PMID: 11459828.
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    68. Zorio DA, Bentley DL. Transcription elongation: the 'Foggy' is liftingellipsis. Curr Biol. 2001 Feb 20; 11(4):R144-6. PMID: 11250170.
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    69. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Bl?cker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15; 409(6822):860-921. PMID: 11237011.
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    70. Schroeder SC, Schwer B, Shuman S, Bentley D. Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev. 2000 Oct 01; 14(19):2435-40. PMID: 11018011.
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    71. Mayer K, Sch?ller C, Wambutt R, Murphy G, Volckaert G, Pohl T, D?sterh?ft A, Stiekema W, Entian KD, Terryn N, Harris B, Ansorge W, Brandt P, Grivell L, Rieger M, Weichselgartner M, de Simone V, Obermaier B, Mache R, M?ller M, Kreis M, Delseny M, Puigdomenech P, Watson M, Schmidtheini T, Reichert B, Portatelle D, Perez-Alonso M, Boutry M, Bancroft I, Vos P, Hoheisel J, Zimmermann W, Wedler H, Ridley P, Langham SA, McCullagh B, Bilham L, Robben J, Van der Schueren J, Grymonprez B, Chuang YJ, Vandenbussche F, Braeken M, Weltjens I, Voet M, Bastiaens I, Aert R, Defoor E, Weitzenegger T, Bothe G, Ramsperger U, Hilbert H, Braun M, Holzer E, Brandt A, Peters S, van Staveren M, Dirske W, Mooijman P, Klein Lankhorst R, Rose M, Hauf J, K?tter P, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Van den Daele H, De Keyser A, Buysshaert C, Gielen J, Villarroel R, De Clercq R, Van Montagu M, Rogers J, Cronin A, Quail M, Bray-Allen S, Clark L, Doggett J, Hall S, Kay M, Lennard N, McLay K, Mayes R, Pettett A, Rajandream MA, Lyne M, Benes V, Rechmann S, Borkova D, Bl?cker H, Scharfe M, Grimm M, L?hnert TH, Dose S, de Haan M, Maarse A, Sch?fer M, M?ller-Auer S, Gabel C, Fuchs M, Fartmann B, Granderath K, Dauner D, Herzl A, Neumann S, Argiriou A, Vitale D, Liguori R, Piravandi E, Massenet O, Quigley F, Clabauld G, M?ndlein A, Felber R, Schnabl S, Hiller R, Schmidt W, Lecharny A, Aubourg S, Chefdor F, Cooke R, Berger C, Montfort A, Casacuberta E, Gibbons T, Weber N, Vandenbol M, Bargues M, Terol J, Torres A, Perez-Perez A, Purnelle B, Bent E, Johnson S, Tacon D, Jesse T, Heijnen L, Schwarz S, Scholler P, Heber S, Francs P, Bielke C, Frishman D, Haase D, Lemcke K, Mewes HW, Stocker S, Zaccaria P, Bevan M, Wilson RK, de la Bastide M, Habermann K, Parnell L, Dedhia N, Gnoj L, Schutz K, Huang E, Spiegel L, Sehkon M, Murray J, Sheet P, Cordes M, Abu-Threideh J, Stoneking T, Kalicki J, Graves T, Harmon G, Edwards J, Latreille P, Courtney L, Cloud J, Abbott A, Scott K, Johnson D, Minx P, Bentley D, Fulton B, Miller N, Greco T, Kemp K, Kramer J, Fulton L, Mardis E, Dante M, Pepin K, Hillier L, Nelson J, Spieth J, Ryan E, Andrews S, Geisel C, Layman D, Du H, Ali J, Berghoff A, Jones K, Drone K, Cotton M, Joshu C, Antonoiu B, Zidanic M, Strong C, Sun H, Lamar B, Yordan C, Ma P, Zhong J, Preston R, Vil D, Shekher M, Matero A, Shah R, Swaby IK, O'Shaughnessy A, Rodriguez M, Hoffmann J, Till S, Granat S, Shohdy N, Hasegawa A, Hameed A, Lodhi M, Johnson A, Chen E, Marra M, Martienssen R, McCombie WR. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature. 1999 Dec 16; 402(6763):769-77. PMID: 10617198.
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    72. Yankulov K, Todorov I, Romanowski P, Licatalosi D, Cilli K, McCracken S, Laskey R, Bentley DL. MCM proteins are associated with RNA polymerase II holoenzyme. Mol Cell Biol. 1999 Sep; 19(9):6154-63. PMID: 10454562.
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    73. Bentley D. Coupling RNA polymerase II transcription with pre-mRNA processing. Curr Opin Cell Biol. 1999 Jun; 11(3):347-51. PMID: 10395561.
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    74. Bentley D. RNA processing. A tale of two tails. Nature. 1998 Sep 03; 395(6697):21-2. PMID: 9738492.
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    75. McNeil JB, Agah H, Bentley D. Activated transcription independent of the RNA polymerase II holoenzyme in budding yeast. Genes Dev. 1998 Aug 15; 12(16):2510-21. PMID: 9716404.
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    76. Yankulov K, Bentley D. Transcriptional control: Tat cofactors and transcriptional elongation. Curr Biol. 1998 Jun 18; 8(13):R447-9. PMID: 9651670.
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    77. Ho CK, Sriskanda V, McCracken S, Bentley D, Schwer B, Shuman S. The guanylyltransferase domain of mammalian mRNA capping enzyme binds to the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem. 1998 Apr 17; 273(16):9577-85. PMID: 9545288.
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    78. McCracken S, Rosonina E, Fong N, Sikes M, Beyer A, O'Hare K, Shuman S, Bentley D. Role of RNA polymerase II carboxy-terminal domain in coordinating transcription with RNA processing. Cold Spring Harb Symp Quant Biol. 1998; 63:301-9. PMID: 10384294.
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    79. McCracken S, Fong N, Rosonina E, Yankulov K, Brothers G, Siderovski D, Hessel A, Foster S, Shuman S, Bentley DL. 5'-Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II. Genes Dev. 1997 Dec 15; 11(24):3306-18. PMID: 9407024.
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    80. Yankulov KY, Bentley DL. Regulation of CDK7 substrate specificity by MAT1 and TFIIH. EMBO J. 1997 Apr 01; 16(7):1638-46. PMID: 9130709.
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    81. McCracken S, Fong N, Yankulov K, Ballantyne S, Pan G, Greenblatt J, Patterson SD, Wickens M, Bentley DL. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature. 1997 Jan 23; 385(6614):357-61. PMID: 9002523.
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    82. Akhtar A, Faye G, Bentley DL. Distinct activated and non-activated RNA polymerase II complexes in yeast. EMBO J. 1996 Sep 02; 15(17):4654-64. PMID: 8887556.
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    83. Yankulov KY, Pandes M, McCracken S, Bouchard D, Bentley DL. TFIIH functions in regulating transcriptional elongation by RNA polymerase II in Xenopus oocytes. Mol Cell Biol. 1996 Jul; 16(7):3291-9. PMID: 8668144.
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    84. Blau J, Xiao H, McCracken S, O'Hare P, Greenblatt J, Bentley D. Three functional classes of transcriptional activation domain. Mol Cell Biol. 1996 May; 16(5):2044-55. PMID: 8628270.
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    85. Yankulov K, Yamashita K, Roy R, Egly JM, Bentley DL. The transcriptional elongation inhibitor 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole inhibits transcription factor IIH-associated protein kinase. J Biol Chem. 1995 Oct 13; 270(41):23922-5. PMID: 7592583.
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    86. Bentley DL. Regulation of transcriptional elongation by RNA polymerase II. Curr Opin Genet Dev. 1995 Apr; 5(2):210-6. PMID: 7613091.
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    87. Yankulov K, Blau J, Purton T, Roberts S, Bentley DL. Transcriptional elongation by RNA polymerase II is stimulated by transactivators. Cell. 1994 Jun 03; 77(5):749-59. PMID: 8205623.
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    88. Roberts S, Purton T, Bentley DL. A protein-binding site in the c-myc promoter functions as a terminator of RNA polymerase II transcription. Genes Dev. 1992 Aug; 6(8):1562-74. PMID: 1644297.
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    89. Roberts S, Bentley DL. Distinct modes of transcription read through or terminate at the c-myc attenuator. EMBO J. 1992 Mar; 11(3):1085-93. PMID: 1372247.
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    90. Casimir CM, Bu-Ghanim HN, Rodaway AR, Bentley DL, Rowe P, Segal AW. Autosomal recessive chronic granulomatous disease caused by deletion at a dinucleotide repeat. Proc Natl Acad Sci U S A. 1991 Apr 01; 88(7):2753-7. PMID: 2011585.
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    91. Rodaway AR, Teahan CG, Casimir CM, Segal AW, Bentley DL. Characterization of the 47-kilodalton autosomal chronic granulomatous disease protein: tissue-specific expression and transcriptional control by retinoic acid. Mol Cell Biol. 1990 Oct; 10(10):5388-96. PMID: 2398896.
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    92. Bentley DL, Brown WL, Groudine M. Accurate, TATA box-dependent polymerase III transcription from promoters of the c-myc gene in injected Xenopus oocytes. Genes Dev. 1989 Aug; 3(8):1179-89. PMID: 2792759.
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    93. Bentley DL, Groudine M. Sequence requirements for premature termination of transcription in the human c-myc gene. Cell. 1988 Apr 22; 53(2):245-56. PMID: 2834065.
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    94. Hann SR, King MW, Bentley DL, Anderson CW, Eisenman RN. A non-AUG translational initiation in c-myc exon 1 generates an N-terminally distinct protein whose synthesis is disrupted in Burkitt's lymphomas. Cell. 1988 Jan 29; 52(2):185-95. PMID: 3277717.
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    95. Cesarman E, Dalla-Favera R, Bentley D, Groudine M. Mutations in the first exon are associated with altered transcription of c-myc in Burkitt lymphoma. Science. 1987 Nov 27; 238(4831):1272-5. PMID: 3685977.
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    96. Bentley DL, Groudine M. Novel promoter upstream of the human c-myc gene and regulation of c-myc expression in B-cell lymphomas. Mol Cell Biol. 1986 Oct; 6(10):3481-9. PMID: 3540591.
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    97. Bentley DL, Groudine M. A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells. Nature. 1986 Jun 12-18; 321(6071):702-6. PMID: 3520340.
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    98. Bentley DL, Farrell PJ, Rabbitts TH. Unrearranged immunoglobulin variable region genes have a functional promoter. Nucleic Acids Res. 1982 Mar 25; 10(6):1841-56. PMID: 6210879.
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