David Bentley, PhD

Publications

• Johnson, S. Cubberley, G. and Bentley, D. (2009) Co-transcriptional recruitment of the mRNA export factor Yra1 by direct interaction with the 3'-end processing factor Pcf11 Mol. Cell. 33:215-226.
• Glover-Cutter, K., Larochelle, S., Erickson, B., Zhang, C., Shokat, K., Fisher, R.P., and Bentley, D.L. (2009). TFIIH-associated Cdk7 kinase functions in phosphorylation of CTD Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase II. Mol Cell Biol 29, 5455-5464.
• Fong, N., Ohman, M., and Bentley, D.L. (2009). Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing. Nat Struct Mol Biol 16, 916-922.
• Perales, R. and Bentley D. (2009) “Co-transcriptionality” - the transcription elongation complex as a nexus for nuclear transactions Mol. Cell. 36:178-191.
• Kim, H. Erickson, B. Luo, W. Seward, D. Graber, J. Pollock, D. Megee, P. Bentley D. (2010) Gene-specific RNA pol II phosphorylation and the CTD code, Nat Struct Mol Biol. 17: 1279-1286.
• Johnson, S.A., Kim, H., Erickson, B., and Bentley, D.L. (2011). The export factor Yra1 modulates mRNA 3' end processing. Nat Struct Mol Biol 18, 1164-1171.
• Kim, S., Kim, H., Fong, N., Erickson, B., and Bentley, D.L. (2011). Pre-mRNA splicing is a determinant of histone H3K36 methylation. Proc Natl Acad Sci U S A 108, 13564-13569.
• Perales, R., Zhang, L., and Bentley, D. (2011). Histone occupancy in vivo at the 601 nucleosome binding element is determined by transcriptional history. Mol Cell Biol 31, 3485-3496.
• Brannan, K., Kim, H., Erickson, B., Glover-Cutter, K., Kim, S., Fong, N., Kiemele, L., Hansen, K., Davis, R., Lykke-Andersen, J., and Bentley, D. (2012). mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. Mol. Cell 46.
• Brannan, K., and Bentley, D. (2012). Control of Transcriptional Elongation by RNA polymerase II: A retrospective. Genetics Res Intl, Article ID 170173
• Brannan, K., Kim, H., Erickson, B., Glover-Cutter, K., Kim, S., Fong, N., Kiemele, L., Hansen, K., Davis, R., Lykke-Andersen, J. et al. 2012. mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. Molecular Cell 46: 311-324.
• Brannan, K. and Bentley, D. 2012. Control of Transcriptional Elongation by RNA polymerase II: A retrospective. Genetics Res Intl: Article ID 170173
• Larochelle S, Amat R, Glover-Cutter K, Sansó M, Zhang C, Allen JJ, Shokat KM, Bentley D, Fisher RP. Cyclin-dependent kinase control of the initiation-to-elongation switch of RNA polymerase II, Nat Struct Mol Biol. 2012 Oct 14. doi: 10.1038/nsmb.2399
• 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 1;28(23):2663-76. PubMed PMID: 25452276
• Bentley DL. Coupling mRNA processing with transcription in time and space. Nat Rev Genet. 2014 Mar;15(3):163-75. PubMed PMID: 24514444
• 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. 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. PubMed PMID: 24412361
• Perales, R., Erickson, B., Zhang, L., Kim, H., Valiquett, E., and Bentley, D. (2013). Gene promoters dictate histone occupancy within genes. EMBO J. 32:2645-2656 PMCID: PMC3791371
• 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. PubMed PMID: 26474067
• Bentley, D.L. (2014). Coupling mRNA processing with transcription in time and space. Nat Rev Genet 15, 163-175. PMID:24514444
• 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 Aug 1;20(5):1173-1186. PubMed PMID: 28768201
• 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 Sep 15;77(18):4934-4946. PubMed PMID: 28729413
• 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. PubMed PMID: 28506463
• 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 Jan 3;73(1):107-118.e4. PubMed PMID: 30503775
• Erickson B, Sheridan RM, Cortazar M, Bentley DL. Dynamic turnover of paused Pol II complexes at human promoters. Genes Dev. 2018 Sep 1;32(17-18):1215-1225. PubMed PMID: 30150253
• Saldi T, Fong N, Bentley DL. Transcription elongation rate affects nascent histone pre-mRNA folding and 3' end processing. Genes Dev. 2018 Feb 1;32(3-4):297-308. PubMed PMID: 29483154
• 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 Dec 19;76(6):896-908.e4. PubMed PMID: 31677974
• 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 Jan 3;73(1):107-118.e4. PubMed PMID: 30503775
• 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 Oct 15. [Epub ahead of print] PubMed PMID: 33060135
• 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. PubMed PMID: 34174817
• 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 Apr 15;81(8):1789-1801.e5. PubMed PMID: 33631106
• Geisberg JV, Moqtaderi Z, Fong N, Erickson B, Bentley DL, Struhl K. Nucleotide-level linkage of transcriptional elongation and polyadenylation. Elife. 2022 Nov 24;11. PubMed PMID: 36421680
• 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 Oct 1;36(19-20):1062-1078. PubMed PMID: 36396340
• 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 Oct 6;82(19):3632-3645.e4. PubMed PMID: 36206739
• Cortázar 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. PubMed PMID: 37753464
• Cozzolino K, Sanford L, Hunter S, Molison K, Erickson B, Jones T, 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. 2023 Dec 13. PubMed PMID: 37461585
• Shenasa H, Bentley DL. Pre-mRNA splicing and its cotranscriptional connections. Trends Genet. 2023 Sep;39(9):672-685. PubMed PMID: 37236814