Publications

Hada A, Hota SK, Luo J, Lin YC, Kale S, Shaytan AK, Bhardwaj SK, Persinger J, Ranish J, Panchenko AR, Bartholomew B.  Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling. Cell Rep. 2019 Jul 2;28(1):282-294.e6. 

He W, Zhang L, Villarreal OD, Fu R, Bedford E, Dou J, Patel AY, Bedford MT, Shi X, Chen T, Bartholomew B, Xu H.  De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. Nat Commun. 2019 Oct 4;10(1):4541. 

Paul S, Bartholomew B. Regulation of ATP-dependent chromatin remodelers: accelerators/brakes, anchors and sensors. Biochem Soc Trans. 2018 Dec 17;46(6):1423-1430. 

Brahma S, Ngubo M, Paul S, Udugama M, Bartholomew B. The Arp8 and Arp4 module acts as a DNA sensor controlling INO80 chromatin remodeling. Nat Commun. 2018 Aug 17;9(1):3309. 

Meng H, Bartholomew B. Emerging Roles of Transcriptional Enhancers In Chromatin Looping And Promoter-Proximal Pausing Of RNA Polymerase II. J Biol Chem. 2018 Sep 7;293(36):13786-13794. Review.

Bartholomew B. Proteasomes beyond proteolysis: Roles in heterochromatin maintenance. J Biol Chem. 2017 Oct 13;292(41):17156-17157

Brahma S, Udugama MI, Kim J, Hada A, Bhardwaj SK, Hailu SG, Lee TH, Bartholomew B. INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers. Nat Commun. 2017 Jun 12;8:15616. 

Sen P, Luo J, Hada A, Hailu SG, Dechassa ML, Persinger J, Brahma S, Paul S, Ranish J, Bartholomew B. Loss of Snf5 Induces Formation of an Aberrant SWI/SNF Complex. Cell Rep. 2017 Feb 28;18(9):2135-2147. 

Prasad R, D'Arcy S, Hada A, Luger K, Bartholomew B. Coordinated action of Nap1 and RSC in disassembly of tandem nucleosomes. Mol Cell Biol. 2016 Aug 12;36(17):2262-7.

Harada BT, Hwang WL, Deindl S, Chatterjee N, Bartholomew B, Zhuang X. Stepwise nucleosome translocation by RSC remodeling complexes. Elife. 2016 Feb 19;5. pii: e10051.

Lafon A, Taranum S, Peitrocola F, Dingli F, Loew D, Brahma S, Bartholomew B, Papmichos-Chronakis M.  INO80 chromatin remodeler facilitates release of RNA polymerase II from chromatin for ubiquitin mediated proteosomal degradation. Mol Cell. 2015 Dec 3;60(5):784-96. 

Chatterjee N, North JA, Dechassa ML, Manohar M, Prasad R, Luger K, Ottesen JJ, Poiier MG, Bartholomew B. Histone acetylation near the nucleosome dyad axis enhances nucleosome disassembly by RSC and SWI/SNF. Mol Cell Biol. 2015 Dec;35(23):4083-92.

Li M, Hada A, Sen P, Olufemi L, Hall MA, Smith BY, Forth S, McKnight JN, Patel A, Bowman GD, Bartholomew B, Wang MD. Dynamic regulation of transcription factors by nucleosome remodeling. Elife. 2015 Jun 5;4. 

Kim SA, Chatterjee N, Jennings MJ, Bartholomew B, Tan S. Extranucleosomal DNA enhances the activity of the LSD1/CoREST histone demethylase complex. Nucleic Acids Res. 2015 May 26;43(10):4868-80. 

Kapoor P, Bao Y, Xiao J, Luo J, Shen J, Persinger J, Peng G, Ranish J, Bartholomew B, Shen X. Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex. Genes Dev. 2015 Mar 15;29(6):591-602. 

Creamer KM, Job G, Shankar S, Neale GA, Lin YC, Bartholomew B, Partridge JF. The Mi-2 homolog Mit1 Actively Positions Nucleosomes within Heterochromatin to Suppress Transcription. Mol Cell Biol. 2014 Jun;34(11):2046-61.

Bartholomew B. Regulating the Chromatin Landscape: Structural and Mechanistic Perspectives. Annu Rev Biochem. 2014;83:671-96.

Bartholomew B. ISW chromatin remodeling: one primary actor or a coordinated effort. Curr Opin Struct Biol. 2014 Feb;24:150-5.

Bartholomew B. Monomeric actin required for INO80 remodeling. Nat Struct Mol Biol. 2013 Apr;20(4):405-7.

Deindl S, Hwang WL, Hota SK, Blosser TR, Prasad P, Bartholomew B, Zhuang X.  ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps. Cell. 2013 Jan 31;152(3):442-52.

Hota SK, Bhardwaj SK, Deindl S, Lin YC, Zhuang X, Bartholomew B (2013). Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains. at Struct Mol Biol. 2013 Feb;20(2):222-9

Sen P, Vivas P, Dechassa ML, Mooney AM, Poirier MG, Bartholomew B. The SnAC domain of SWI/SNF is a Histone Anchor Required for Remodeling. Mol Cell Biol. 2013 Jan;33(2):360-70.

Dechassa ML, Hota SK, Sen P, Chatterjee N, Prasad P, and Bartholomew B. Disparity in the DNA translocase domains of SWI/SNF and ISW2. Nucleic Acids Res. 2012 May;40(10):4412-21.

Darst RP, Pardo CE, Pondugula S, Gangaraju VK, Nabilsi NH, Bartholomew B, Kladde MP.  Simultaneous single-molecule detection of endogenous C-5 DNA methylation and chromatin accessibility using MAPit. Methods Mol Biol. 2012;833:125-41

Hota SK, Dechassa ML, Prasad P, Bartholomew B. Mapping Protein-DNA and Protein-Protein Interactions of ATP-dependent Chromatin Remodelers. Methods Mol Biol. 2012;809:381-409.

Hota SK, Bartholomew B. Approaches for Studying Nucleosome Movement by ATP-dependent Chromatin Remodeling Complexes. Methods Mol Biol. 2012;809:367-80.

Sen P, Ghosh S,  Pugh BF, Bartholomew B. A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling. Nucleic Acids Res. 2011 Nov;39(21):9155-66.  

Chatterjee N, Sinha D, Lemma-Dechassa M, Tan S, Shogren-Knaak MA, Bartholomew B. Histone H3 tail acetylation modulates ATP-dependent remodeling through multiple mechanisms. Nucleic Acids Res. 2011 Oct;39(19):8378-91.

Hota SK, Bartholomew B. Diversity of operation in ATP-dependent chromatin remodelers. Biochim Biophys Acta. 2011 Sep;1809(9):476-87.

North JA, Javaid S, Ferdinand MB, Chatterjee N, Picking JW, Shoffner M, Nakkula RJ, Bartholomew B, Ottesen JJ, Fishel R, Poirier MG. Phosphorylation of histone H3(T118) alters nucleosome dynamics and remodeling. Nucleic Acids Res. 2011 Aug;39(15):6465-74.

Gaykalova DA, Nagarajavel V,  Bondarenko VA,  Bartholomew B,  Clark DJ, Studitsky VM. A polar barrier to transcription can be circumvented by remodeler-induced nucleosome translocation. Nucleic Acids Res. 2011 May;39(9):3520-8. 

Udugama M, Sabri A, Bartholomew B. The INO80 ATP-dependent chromatin remodeling complex is a nucleosome spacing factor. Mol Cell Biol. 2011 Feb;31(4):662-73.

Dechassa ML, Sabri A, Pondugula S,  Kassabov SR, Chatterjee N, Kladde MP, Bartholomew B. SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes. Mol Cell. 2010 May 28;38(4):590-602.

Prasad P, Bartholomew B. Control of nucleosome movement – to space or not to space nucleosomes? Epigenetics. 2010 May 16;5(4):282-6.

Gangaraju VK, Prasad P, Srour A, Kagalwala MN, Bartholomew B. Conformational changes associated with template commitment in ATP-dependent chromatin remodeling by ISW2. Mol Cell. 2009 Jul 10;35(1):58-69.

Ransom M, Williams SK, Dechassa ML, Das C, Linger J, Adkins M, Liu C, Bartholomew B, JK Tyler. FACT and the proteasome promote promoter chromatin disassembly and transcriptional initiation. J Biol Chem. 2009 Aug 28;284(35):23461-71.

Persinger J, Bartholomew B. Site-directed DNA crosslinking of large multisubunit protein-DNA complexes. Methods Mol Biol. 2009;543:453-74.

Dechassa ML, Zhang B, Horowitz-Scherer R, Persinger J, Woodcock CL, Peterson CL, Bartholomew B.  Architecture of the SWI/SNF-nucleosome complex. Mol Cell Biol. 2008 Oct;28(19):6010-21.

Dang W, Bartholomew B. Domain architecture of the catalytic subunit in the ISW2-nucleosome complex. Mol Cell Biol. 2007 Dec;27(23):8306-17.  

Dang W, Kagalwala MN, Bartholomew B. The Dpb4 subunit of ISW2 is anchored to extranucleosomal DNA. J Biol Chem. 2007 Jul 6;282(27):19418-25.

Gangaraju VK, Bartholomew B. Mechanisms of ATP dependent chromatin remodeling. Mutat Res. 2007 May 1;618(1-2):3-17

Gangaraju VK, Bartholomew B. Molecular basis of nucleosome spacing: Two different modes of ISW1a binding to nucleosomes. Mol Cell Biol. 2007 Apr;27(8):3217-25. 

Dang W,  Kagalwala MN, Bartholomew B. Regulation of ISW2 by concerted action of histone H4 tail and extranucleosomal DNA. Mol Cell Biol. 2006 Oct;26(20):7388-96.

Zofall M, Persinger J, Kassabov SR, Bartholomew B. Chromatin remodeling by ISW2 and SWI/SNF require DNA translocation inside the nucleosome. Nat Struct Mol Biol. 2006 Apr;13(4):339-46.

Zofall M, Persinger J, Bartholomew B. Functional role of extranucleosomal DNA and the entry site of the nucleosome in chromatin remodeling by ISW2. Mol Cell Biol. 2004 Nov;24(22):10047-57.

Auty R, Steen H, Myers LC, Persinger J, Bartholomew B, Gygi SP, Buratowski S. Purification of active TFIID from Saccharomyces cerevisiae. Extensive promoter contacts and co-activator function. J Biol Chem. 2004 Nov 26;279(48):49973-81.

Kagalwala MN, Glaus BJ,  Dang W,  Zofall M, Bartholomew B. Topography of the ISW2-Nucleosome Complex: Insights into the Mechanism of ATP-dependent Chromatin Remodeling by ISW2. EMBO J. 2004 May 19;23(10):2092-104.

Kassabov SK, Zhang B, Persinger J, Bartholomew B. SWI/SNF Unwraps, Slides and Rewraps the Nucleosome. Mol Cell. 2003 Feb;11(2):391-403.

Vary JC Jr, Gangaraju VK, Qin J, Landel CC, Kooperberg C, Bartholomew B, Tsukiyama T. Yeast Isw1p forms two separable complexes in vivo. Mol Cell Biol. 2003 Jan;23(1):80-91.

Kassabov SK, Henry NH, Zofall M, Tsukiyama T, Bartholomew B. High-resolution Mapping of Changes in Histone-DNA Contacts of Nucleosomes Remodeled by ISW2. Mol Cell Biol. 2002 Nov;22(21):7524-34.

Persinger J, Bartholomew B. Site-directed DNA photoaffinity labeling of RNA polymerase III transcription complexes. Methods Mol Biol. 2001;148:363-81. 

Sengupta SM, VanKanegan M, Persinger J, Logie C, Cairns BR, Peterson CL, Bartholomew B. The Interactions of Yeast SWI/SNF and RSC with the Nucleosome Before and After Chromatin Remodeling. J Biol Chem. 2001 Apr 20;276(16):12636-44.

Zofall M, Bartholomew B. Two Novel dATP Analogues for DNA Photoaffinity Labeling. Nucleic Acids Res. 2000 Nov 1;28(21):4382-90.

Sengupta SM, Persinger J, Bartholomew B, Peterson CL. Use of DNA photoaffinity labeling to study nucleosome remodeling by SWI/SNF. Methods. 1999 Nov;19(3):434-46.

Persinger J, Sengupta SM, Bartholomew B. Spatial Organization of the Core Region of Yeast TFIIIB-DNA Complexes. Mol Cell Biol. 1999 Jul;19(7):5218-34.

Michelson RJ, Collard MW, Ziemba AJ, Persinger J, Bartholomew B, Huggenvik JI. Nuclear DEAF-1 related (NUDR) Protein Contains a Novel DNA Binding Domain and Represses Transcription of the Heterogeneous Nuclear Ribonucleoprotein A2/B1 Promoter. J Biol Chem. 1999 Oct 22;274(43):30510-9.

Tate JJ, Persinger J, Bartholomew B. Survey of four different photoreactive moieties for DNA photoaffinity labeling of yeast RNA polymerase III transcription complexes. Nucleic Acids Res. 1998 Mar 15;26(6):1421-6.

Radebaugh CA, Gong X, Bartholomew B, Paule MR. Identification of Previously Unrecognized Common Elements in Eukaryotic Promoters: a Ribosomal RNA Initiator Element for RNA Polymerase I. J Biol Chem. 1997 Feb 7;272(6):3141-4.

Persinger J, Bartholomew B. Mapping the Contacts of Yeast TFIIIB and RNA Polymerase III at Various Distances from the Major Groove of DNA by DNA Photoaffinity Labeling. J Biol Chem. 1996 Dec 20;271(51):33039-46.

Pruss D, Bartholomew B, Persinger J, Hayes J, Arents G, Moudrianakis EN, Wolffe AP. An asymmetric model for the nucleosome: a binding site for linker histones inside the DNA gyres. Science. 1996 Oct 25;274(5287):614-7.

Powell W, Bartholomew B, Rienes D. Elongation Factor SII Contacts the 3' End of RNA in RNA Polymerase II Elongation Complex. J Biol Chem. 1996 Sep 13;271(37):22301-4.

Lannutti BJ, Persinger J, Bartholomew B. Probing the protein-DNA Contacts of a Yeast RNA Polymerase III Transcription Complex in a Crude Extract: Solid Phase Synthesis of DNA Photoaffinity Probes Containing a Novel Photoreactive Deoxycytidine Analog. Biochemistry. 1996 Jul 30;35(30):9821-31.

Bartholomew B, Tinker RL, Kassavetis GA, Geiduschek EP. Photochemical Cross-linking Assay for DNA Tracking by Replication Proteins. Methods Enzymol. 1995;262:476-94.

Bartholomew B, Braun BR, Kassavetis GA, Geiduschek EP. Probing Close DNA Contacts of RNA Polymerase III Transcription Complexes with the Photoactive Nucleoside 4-Thiodeoxythymidine. J Biol Chem. 1994 Jul 8;269(27):18090-5.

Bartholomew B, Durkovich D, Kassavetis GA, Geiduschek EP. Orientation and Topography of RNA Polymerase III in Transcription Complexes. Mol Cell Biol. 1993 Feb;13(2):942-52.

Braun BR, Bartholomew B, Kassavetis GA, Geiduschek EP. Topography of transcription factor complexes on the Saccharomyces cerevisiae 5 S RNA gene. J Mol Biol. 1992 Dec 20;228(4):1063-77.

Bartholomew B, Kassavetis GA, Geiduschek EP. Two components of Saccharomyces cerevisiae transcription factor IIIB (TFIIIB) are stereospecifically located upstream of a tRNA gene and interact with the second-largest subunit of TFIIIC. Mol Cell Biol. 1991 Oct;11(10):5181-9.

Kassavetis GA, Bartholomew B, Blanco JA, Johnson TE, Geiduschek EP. Two essential components of the Saccharomyces cerevisiae transcription factor TFIIIB: transcription and DNA binding properties. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7308-12.

Bartholomew B, Kassavetis GA, Braun BR, Geiduschek EP. The subunit structure of Saccharomyces cerevisiae transcription factor IIIC probed with a novel photocrosslinking reagent. EMBO J. 1990 Jul;9(7):2197-205

Bartholomew B, Meares CF, Dahmus ME. Photoaffinity labeling of RNA polymerase III transcription complexes by nascent RNA. J Biol Chem. 1990 Mar 5;265(7):3731-7.

Bartholomew B, Dahmus ME, Meares CF. RNA contacts subunits II0 and IIC in HeLa RNA polymerase II transcription complexes. J Biol Chem. 1986 Oct 25;261(30):14226-31.