My Bibliography

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Francette AM, Arndt KM. Multiple direct and indirect roles of the Paf1 complex in transcription elongation, splicing, and histone modifications. Cell Rep. 2024 Sep 24;43(9):114730. doi: 10.1016/j.celrep.2024.114730. Epub 2024 Sep 7. PubMed PMID: 39244754; PubMed Central PMCID: PMC11498942.

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Fetian T, Grover A, Arndt KM. Histone H2B ubiquitylation: Connections to transcription and effects on chromatin structure. Biochim Biophys Acta Gene Regul Mech. 2024 Jun;1867(2):195018. doi: 10.1016/j.bbagrm.2024.195018. Epub 2024 Feb 6. Review. PubMed PMID: 38331024; PubMed Central PMCID: PMC11098702.

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Ellison MA, Namjilsuren S, Shirra MK, Blacksmith MS, Schusteff RA, Kerr EM, Fang F, Xiang Y, Shi Y, Arndt KM. Spt6 directly interacts with Cdc73 and is required for Paf1 complex occupancy at active genes in Saccharomyces cerevisiae. Nucleic Acids Res. 2023 Jun 9;51(10):4814-4830. doi: 10.1093/nar/gkad180. PubMed PMID: 36928138; PubMed Central PMCID: PMC10250246.

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Fetian T, McShane BM, Horan NL, Shodja DN, True JD, Mosley AL, Arndt KM. Paf1 complex subunit Rtf1 stimulates H2B ubiquitylation by interacting with the highly conserved N-terminal helix of Rad6. Proc Natl Acad Sci U S A. 2023 May 30;120(22):e2220041120. doi: 10.1073/pnas.2220041120. Epub 2023 May 22. PubMed PMID: 37216505; PubMed Central PMCID: PMC10235976.

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Shirra MK, Kocik RA, Ellison MA, Arndt KM. Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription in Saccharomyces cerevisiae. G3 (Bethesda). 2021 Oct 19;11(11). doi: 10.1093/g3journal/jkab298. PubMed PMID: 34499735; PubMed Central PMCID: PMC8527469.

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Kaplan CD, Arndt KM. A PICture is worth a thousand words (and ten references). Cell. 2021 Jul 22;184(15):3850-3851. doi: 10.1016/j.cell.2021.06.030. PubMed PMID: 34297929.

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Francette AM, Tripplehorn SA, Arndt KM. The Paf1 Complex: A Keystone of Nuclear Regulation Operating at the Interface of Transcription and Chromatin. J Mol Biol. 2021 Jul 9;433(14):166979. doi: 10.1016/j.jmb.2021.166979. Epub 2021 Apr 1. Review. PubMed PMID: 33811920; PubMed Central PMCID: PMC8184591.

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Ellison MA, Walker JL, Ropp PJ, Durrant JD, Arndt KM. MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations. G3 (Bethesda). 2020 Sep 2;10(9):3009-3014. doi: 10.1534/g3.120.401396. PubMed PMID: 32605926; PubMed Central PMCID: PMC7466961.

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Hildreth AE, Ellison MA, Francette AM, Seraly JM, Lotka LM, Arndt KM. The nucleosome DNA entry-exit site is important for transcription termination and prevention of pervasive transcription. Elife. 2020 Aug 26;9. doi: 10.7554/eLife.57757. PubMed PMID: 32845241; PubMed Central PMCID: PMC7449698.

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Cucinotta CE, Hildreth AE, McShane BM, Shirra MK, Arndt KM. The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo. Nucleic Acids Res. 2019 Sep 19;47(16):8410-8423. doi: 10.1093/nar/gkz549. PubMed PMID: 31226204; PubMed Central PMCID: PMC6895269.

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Ellison MA, Lederer AR, Warner MH, Mavrich TN, Raupach EA, Heisler LE, Nislow C, Lee MT, Arndt KM. The Paf1 Complex Broadly Impacts the Transcriptome of Saccharomyces cerevisiae. Genetics. 2019 Jul;212(3):711-728. doi: 10.1534/genetics.119.302262. Epub 2019 May 15. PubMed PMID: 31092540; PubMed Central PMCID: PMC6614894.

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Hildreth AE, Arndt KM. A transcriptional switch controls meiosis. Elife. 2017 Oct 24;6. doi: 10.7554/eLife.31911. PubMed PMID: 29063829; PubMed Central PMCID: PMC5655149.

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Van Oss SB, Cucinotta CE, Arndt KM. Emerging Insights into the Roles of the Paf1 Complex in Gene Regulation. Trends Biochem Sci. 2017 Oct;42(10):788-798. doi: 10.1016/j.tibs.2017.08.003. Epub 2017 Sep 1. Review. PubMed PMID: 28870425; PubMed Central PMCID: PMC5658044.

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Van Oss SB, Shirra MK, Bataille AR, Wier AD, Yen K, Vinayachandran V, Byeon IL, Cucinotta CE, Héroux A, Jeon J, Kim J, VanDemark AP, Pugh BF, Arndt KM. The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6. Mol Cell. 2016 Nov 17;64(4):815-825. doi: 10.1016/j.molcel.2016.10.008. Epub 2016 Nov 10. PubMed PMID: 27840029; PubMed Central PMCID: PMC5131541.

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Raupach EA, Martens JA, Arndt KM. Evidence for Regulation of ECM3 Expression by Methylation of Histone H3 Lysine 4 and Intergenic Transcription in Saccharomyces cerevisiae. G3 (Bethesda). 2016 Sep 8;6(9):2971-81. doi: 10.1534/g3.116.033118. PubMed PMID: 27449519; PubMed Central PMCID: PMC5015954.

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Cucinotta CE, Arndt KM. SnapShot: Transcription Elongation. Cell. 2016 Aug 11;166(4):1058-1058.e1. doi: 10.1016/j.cell.2016.07.039. PubMed PMID: 27518568.

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Cucinotta CE, Young AN, Klucevsek KM, Arndt KM. The Nucleosome Acidic Patch Regulates the H2B K123 Monoubiquitylation Cascade and Transcription Elongation in Saccharomyces cerevisiae. PLoS Genet. 2015 Aug;11(8):e1005420. doi: 10.1371/journal.pgen.1005420. eCollection 2015 Aug. PubMed PMID: 26241481; PubMed Central PMCID: PMC4524731.

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Arndt KM, Reines D. Termination of Transcription of Short Noncoding RNAs by RNA Polymerase II. Annu Rev Biochem. 2015;84:381-404. doi: 10.1146/annurev-biochem-060614-034457. Epub 2015 Mar 26. Review. PubMed PMID: 25747400; PubMed Central PMCID: PMC5104496.

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Wier AD, Mayekar MK, Héroux A, Arndt KM, VanDemark AP. Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin. Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):17290-5. doi: 10.1073/pnas.1314754110. Epub 2013 Oct 7. PubMed PMID: 24101474; PubMed Central PMCID: PMC3808610.

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Mayekar MK, Gardner RG, Arndt KM. The recruitment of the Saccharomyces cerevisiae Paf1 complex to active genes requires a domain of Rtf1 that directly interacts with the Spt4-Spt5 complex. Mol Cell Biol. 2013 Aug;33(16):3259-73. doi: 10.1128/MCB.00270-13. Epub 2013 Jun 17. PubMed PMID: 23775116; PubMed Central PMCID: PMC3753903.

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Tomson BN, Crisucci EM, Heisler LE, Gebbia M, Nislow C, Arndt KM. Effects of the Paf1 complex and histone modifications on snoRNA 3'-end formation reveal broad and locus-specific regulation. Mol Cell Biol. 2013 Jan;33(1):170-82. doi: 10.1128/MCB.01233-12. Epub 2012 Oct 29. PubMed PMID: 23109428; PubMed Central PMCID: PMC3536304.

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Tomson BN, Arndt KM. The many roles of the conserved eukaryotic Paf1 complex in regulating transcription, histone modifications, and disease states. Biochim Biophys Acta. 2013 Jan;1829(1):116-26. doi: 10.1016/j.bbagrm.2012.08.011. Epub 2012 Sep 6. PubMed PMID: 22982193; PubMed Central PMCID: PMC3541448.

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Klucevsek KM, Braun MA, Arndt KM. The Paf1 complex subunit Rtf1 buffers cells against the toxic effects of [PSI+] and defects in Rkr1-dependent protein quality control in Saccharomyces cerevisiae. Genetics. 2012 Aug;191(4):1107-18. doi: 10.1534/genetics.112.141713. Epub 2012 May 17. PubMed PMID: 22595241; PubMed Central PMCID: PMC3415995.

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Piro AS, Mayekar MK, Warner MH, Davis CP, Arndt KM. Small region of Rtf1 protein can substitute for complete Paf1 complex in facilitating global histone H2B ubiquitylation in yeast. Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10837-42. doi: 10.1073/pnas.1116994109. Epub 2012 Jun 14. PubMed PMID: 22699496; PubMed Central PMCID: PMC3390850.

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Amrich CG, Davis CP, Rogal WP, Shirra MK, Heroux A, Gardner RG, Arndt KM, VanDemark AP. Cdc73 subunit of Paf1 complex contains C-terminal Ras-like domain that promotes association of Paf1 complex with chromatin. J Biol Chem. 2012 Mar 30;287(14):10863-75. doi: 10.1074/jbc.M111.325647. Epub 2012 Feb 8. PubMed PMID: 22318720; PubMed Central PMCID: PMC3322841.

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Crisucci EM, Arndt KM. Paf1 restricts Gcn4 occupancy and antisense transcription at the ARG1 promoter. Mol Cell Biol. 2012 Mar;32(6):1150-63. doi: 10.1128/MCB.06262-11. Epub 2012 Jan 17. PubMed PMID: 22252319; PubMed Central PMCID: PMC3295010.

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Crisucci EM, Arndt KM. The Paf1 complex represses ARG1 transcription in Saccharomyces cerevisiae by promoting histone modifications. Eukaryot Cell. 2011 Jun;10(6):712-23. doi: 10.1128/EC.05013-11. Epub 2011 Apr 15. PubMed PMID: 21498644; PubMed Central PMCID: PMC3127663.

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Tomson BN, Davis CP, Warner MH, Arndt KM. Identification of a role for histone H2B ubiquitylation in noncoding RNA 3'-end formation through mutational analysis of Rtf1 in Saccharomyces cerevisiae. Genetics. 2011 Jun;188(2):273-89. doi: 10.1534/genetics.111.128645. Epub 2011 Mar 24. PubMed PMID: 21441211; PubMed Central PMCID: PMC3122317.

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Crisucci EM, Arndt KM. The Roles of the Paf1 Complex and Associated Histone Modifications in Regulating Gene Expression. Genet Res Int. 2011;2011. doi: 10.4061/2011/707641. PubMed PMID: 22408743; PubMed Central PMCID: PMC3296560.

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Shirra MK, McCartney RR, Zhang C, Shokat KM, Schmidt MC, Arndt KM. A chemical genomics study identifies Snf1 as a repressor of GCN4 translation. J Biol Chem. 2008 Dec 19;283(51):35889-98. doi: 10.1074/jbc.M805325200. Epub 2008 Oct 27. PubMed PMID: 18955495; PubMed Central PMCID: PMC2602918.

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Rubenstein EM, McCartney RR, Zhang C, Shokat KM, Shirra MK, Arndt KM, Schmidt MC. Access denied: Snf1 activation loop phosphorylation is controlled by availability of the phosphorylated threonine 210 to the PP1 phosphatase. J Biol Chem. 2008 Jan 4;283(1):222-230. doi: 10.1074/jbc.M707957200. Epub 2007 Nov 8. PubMed PMID: 17991748; PubMed Central PMCID: PMC3244878.

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Chu Y, Simic R, Warner MH, Arndt KM, Prelich G. Regulation of histone modification and cryptic transcription by the Bur1 and Paf1 complexes. EMBO J. 2007 Nov 14;26(22):4646-56. doi: 10.1038/sj.emboj.7601887. Epub 2007 Oct 18. PubMed PMID: 17948059; PubMed Central PMCID: PMC2080810.

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Warner MH, Roinick KL, Arndt KM. Rtf1 is a multifunctional component of the Paf1 complex that regulates gene expression by directing cotranscriptional histone modification. Mol Cell Biol. 2007 Sep;27(17):6103-15. doi: 10.1128/MCB.00772-07. Epub 2007 Jun 18. PubMed PMID: 17576814; PubMed Central PMCID: PMC1952162.

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Braun MA, Costa PJ, Crisucci EM, Arndt KM. Identification of Rkr1, a nuclear RING domain protein with functional connections to chromatin modification in Saccharomyces cerevisiae. Mol Cell Biol. 2007 Apr;27(8):2800-11. doi: 10.1128/MCB.01947-06. Epub 2007 Feb 5. PubMed PMID: 17283062; PubMed Central PMCID: PMC1899926.

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Sheldon KE, Mauger DM, Arndt KM. A Requirement for the Saccharomyces cerevisiae Paf1 complex in snoRNA 3' end formation. Mol Cell. 2005 Oct 28;20(2):225-36. doi: 10.1016/j.molcel.2005.08.026. PubMed PMID: 16246725; PubMed Central PMCID: PMC1839845.

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Shirra MK, Rogers SE, Alexander DE, Arndt KM. The Snf1 protein kinase and Sit4 protein phosphatase have opposing functions in regulating TATA-binding protein association with the Saccharomyces cerevisiae INO1 promoter. Genetics. 2005 Apr;169(4):1957-72. doi: 10.1534/genetics.104.038075. Epub 2005 Feb 16. PubMed PMID: 15716495; PubMed Central PMCID: PMC1449608.

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Arndt K, Winston F. An unexpected role for ubiquitylation of a transcriptional activator. Cell. 2005 Mar 25;120(6):733-4. doi: 10.1016/j.cell.2005.03.004. PubMed PMID: 15797373.

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Arndt KM, Kane CM. Running with RNA polymerase: eukaryotic transcript elongation. Trends Genet. 2003 Oct;19(10):543-50. doi: 10.1016/j.tig.2003.08.008. Review. PubMed PMID: 14550628.

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Simic R, Lindstrom DL, Tran HG, Roinick KL, Costa PJ, Johnson AD, Hartzog GA, Arndt KM. Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J. 2003 Apr 15;22(8):1846-56. doi: 10.1093/emboj/cdg179. PubMed PMID: 12682017; PubMed Central PMCID: PMC154471.

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Spencer JV, Arndt KM. A TATA binding protein mutant with increased affinity for DNA directs transcription from a reversed TATA sequence in vivo. Mol Cell Biol. 2002 Dec;22(24):8744-55. doi: 10.1128/MCB.22.24.8744-8755.2002. PubMed PMID: 12446791; PubMed Central PMCID: PMC139874.

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Squazzo SL, Costa PJ, Lindstrom DL, Kumer KE, Simic R, Jennings JL, Link AJ, Arndt KM, Hartzog GA. The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J. 2002 Apr 2;21(7):1764-74. doi: 10.1093/emboj/21.7.1764. PubMed PMID: 11927560; PubMed Central PMCID: PMC125365.

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Shirra MK, Patton-Vogt J, Ulrich A, Liuta-Tehlivets O, Kohlwein SD, Henry SA, Arndt KM. Inhibition of acetyl coenzyme A carboxylase activity restores expression of the INO1 gene in a snf1 mutant strain of Saccharomyces cerevisiae. Mol Cell Biol. 2001 Sep;21(17):5710-22. doi: 10.1128/MCB.21.17.5710-5722.2001. PubMed PMID: 11486011; PubMed Central PMCID: PMC87291.

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Costa PJ, Arndt KM. Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation. Genetics. 2000 Oct;156(2):535-47. doi: 10.1093/genetics/156.2.535. PubMed PMID: 11014804; PubMed Central PMCID: PMC1461271.

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Liu Q, Gabriel SE, Roinick KL, Ward RD, Arndt KM. Analysis of TFIIA function In vivo: evidence for a role in TATA-binding protein recruitment and gene-specific activation. Mol Cell Biol. 1999 Dec;19(12):8673-85. doi: 10.1128/MCB.19.12.8673. PubMed PMID: 10567590; PubMed Central PMCID: PMC85009.

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Shirra MK, Arndt KM. Evidence for the involvement of the Glc7-Reg1 phosphatase and the Snf1-Snf4 kinase in the regulation of INO1 transcription in Saccharomyces cerevisiae. Genetics. 1999 May;152(1):73-87. doi: 10.1093/genetics/152.1.73. PubMed PMID: 10224244; PubMed Central PMCID: PMC1460605.

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Stolinski LA, Eisenmann DM, Arndt KM. Identification of RTF1, a novel gene important for TATA site selection by TATA box-binding protein in Saccharomyces cerevisiae. Mol Cell Biol. 1997 Aug;17(8):4490-500. doi: 10.1128/MCB.17.8.4490. PubMed PMID: 9234706; PubMed Central PMCID: PMC232302.

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Arndt KM, Ricupero-Hovasse S, Winston F. TBP mutants defective in activated transcription in vivo. EMBO J. 1995 Apr 3;14(7):1490-7. doi: 10.1002/j.1460-2075.1995.tb07135.x. PubMed PMID: 7729424; PubMed Central PMCID: PMC398236.

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Arndt KM, Wobbe CR, Ricupero-Hovasse S, Struhl K, Winston F. Equivalent mutations in the two repeats of yeast TATA-binding protein confer distinct TATA recognition specificities. Mol Cell Biol. 1994 Jun;14(6):3719-28. doi: 10.1128/mcb.14.6.3719-3728.1994. PubMed PMID: 8196615; PubMed Central PMCID: PMC358739.

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Eisenmann DM, Arndt KM, Ricupero SL, Rooney JW, Winston F. SPT3 interacts with TFIID to allow normal transcription in Saccharomyces cerevisiae. Genes Dev. 1992 Jul;6(7):1319-31. doi: 10.1101/gad.6.7.1319. PubMed PMID: 1628834.

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Arndt KM, Ricupero SL, Eisenmann DM, Winston F. Biochemical and genetic characterization of a yeast TFIID mutant that alters transcription in vivo and DNA binding in vitro. Mol Cell Biol. 1992 May;12(5):2372-82. doi: 10.1128/mcb.12.5.2372-2382.1992. PubMed PMID: 1569955; PubMed Central PMCID: PMC364409.