Skip to Content

Publications

Articles in Professional Journals

  1. Bartholomew B (2014) Annu Rev Biochem.  Regulating the Chromatin Landscape: Structural and Mechanistic Perspectives.
  2. Bartholomew B (2014)  Curr Opin Struct Biol 24C, 150-155. ISW chromatin remodeling: one primary actor or a coordinated effort
  3. Creamer KM, Job G, Shankar S, Neale GA, Lin YC, Bartholomew B, Partridge JF (2014) Mol Cell Biol 34(11), 2046-61. The Mi-2 homolog Mit1 Actively Positions Nucleosomes within Heterochromatin to Suppress Transcription
  4. Bartholomew B (2013) Nat Struct Mol Biol 20(4), 405-7.  Monomeric actin required for INO80 remodeling.
  5. Sen P, Vivas P, Dechassa ML, Mooney AM, Poirier MG, and Bartholomew (2013) Mol Cell Biol 33(2), 360-70. The SnAC domain of SWI/SNF is a Histone Anchor Required for Remodeling.
  6. Hota SK, Bhardwaj SK, Deindl S, Lin YC, Zhuang X, and Bartholomew B (2013) Nat Struct Mol Biol 20(2):222-9. Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains.
  7. Deindl S, Hota SK, Hwang WL, Blosser TR, Prasad P, Bartholomew B, and Zhuang X (2013) Cell 152(3):442-52. Coordinated stepwise DNA translocation across the nucleosome by ISWI-family remodelers.
  8. Dechassa ML, Hota SK, Sen P, Chatterjee N, Prasad P, and Bartholomew B (2012) Nucleic Acids Res  40(10), 4412-21. Disparity in the DNA translocase domains of SWI/SNF and ISW2.
  9. Darst RP, Pardo CE, Pondugula S, Gangaraju VK, Nabilsi NH, Bartholomew B, Kladde MP (2012) Methods Mol Biol 833, 125-41.  Simultaneous single-molecule detection of endogenous C-5 DNA methylation and chromatin accessibility using MAPit.
  10. Hota SK, Dechassa ML, Prasad P, Bartholomew, B (2012) Methods Mol Biol 809, 381-409. Mapping Protein-DNA and Protein-Protein Interactions of ATP-dependent Chromatin Remodelers.
  11. Hota SK and Bartholomew B (2012) Methods Mol Biol 809, 367-80. Approaches for Studying Nucleosome Movement by ATP-dependent Chromatin Remodeling Complexes.
  12. Sen, P., Ghosh, S.,  Pugh, B.F., and B. Bartholomew, (2011) Nucleic Acids Res 39(21), 9155-66.  A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling  
  13. Gaykalova, DA, Nagarajavel, V,  Bondarenko, VA,  Bartholomew, B,  Clark, DJ, Studitsky, VM (2011) Nucleic Acids Res 39(9), 3520-8.  A polar barrier to transcription can be circumvented by remodeler-induced nucleosome translocation.
  14. North JA, Javaid S, Ferdinand MB, Chatterjee N, Picking JW, Shoffner M, Nakkula RJ, Bartholomew B, Ottesen JJ, Fishel R, Poirier MG. (2011) Nucleic Acids Res 39(15), 6465-74,  Phosphorylation of histone H3(T118) alters nucleosome dynamics and remodeling.
  15. Hota, S.K. and B. Bartholomew, (2011) Biochim. Biophys. Acta, 1809(9), 476-87 Diversity of operation in ATP-dependent chromatin remodelers.
  16. N. Chatterjee, D. Sinha, M. Lemma-Dechassa, S. Tan, M.A. Shogren-Knaak, B. Bartholomew, (2011) Nucleic Acids Res, 39(19), 8378-91. H3 tail acetylation modulates SWI/SNF and RSC activity through multiple mechanisms
  17. Udugama, M., Sabri, A, and B. Bartholomew (2011) Mol Cell Biol 31, 662-673. The INO80 ATP-dependent chromatin remodeling complex is a nucleosome spacing factor.
  18. Gaykalova, DA, Nagarajavel, V,  Bondarenko, VA,  Bartholomew, B,  Clark, DJ, Studitsky, VM (2011) Nucleic Acids Res 39(4), 1-9. A polar barrier to transcription can be circumvented by remodeler-induced nucleosome translocation.
  19. Dechassa ML, Sabri A, Pondugula S,  Kassabov SR, Chatterjee N, Kladde MP and B. Bartholomew (2010) Mol Cell 38(4), 590-602. SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes.
  20. Prasad, P and B. Bartholomew (2010) Epigenetics 5(4), 282-6. Control of nucleosome movement – to space or not to space nucleosomes?
  21. Gangaraju VK, Prasad P, Srour A, Kagalwala MN, and B. Bartholomew (2009) Mol Cell, 35(1), 58-69.  Conformational changes associated with template commitment in ATP-dependent chromatin remodeling by ISW2
  22. Ransom M, Williams SK, Dechassa ML, Das C, Linger J, Adkins M, Liu C, Bartholomew, B, and JK Tyler (2009) J Biol Chem 284(35), 23461-71.  FACT and the proteasome promote promoter chromatin disassembly and transcriptional initiation.
  23. Persinger J and B. Bartholomew (2009) Methods Mol Biol. 543, 453-474. Site-directed DNA crosslinking of large multisubunit protein-DNA complexes.
  24. Dechassa ML, Zhang B, Horowitz-Scherer R, Persinger J, Woodcock CL, Peterson CL, Bartholomew B.  (2008) Mol Cell Biol., 28(19), 6010-21.  Architecture of the SWI/SNF-nucleosome complex.
  25. Dang W. and B. Bartholomew, (2007) Mol Cell Biol,. 27(23), 8306-17. Domain architecture of the catalytic subunit in the ISW2-nucleosome complex.         
  26. Dang. W. Kagalwala MN, Bartholomew B. (2007) J. Biol. Chem 2007. 282(27), 19418-25. The Dpb4 subunit of ISW2 is anchored to extranucleosomal DNA.
  27. Gangaraju, VK and Bartholomew, B (2007) Mutat. Res.  618, 3-17. Mechanisms of ATP dependent chromatin remodeling.
  28. Gangaraju, VK and Bartholomew, B (2007) Mol. Cell. Biol. 27, 3217-25.  Molecular basis of nucleosome spacing: Two different modes of ISW1a binding to nucleosomes.
  29. Zofall, M, Persinger, J., Kassabov, S.R. and Bartholomew (2006) Nat.Struct.Mol.Biol. 13, 339-346. Chromatin remodeling by ISW2 and SWI/SNF require DNA translocation inside the nucleosome.
  30. Dang,W,  Kagalwala, MN, and Bartholomew, B (2006) Mol. Cell. Biol. 26, 7388-96. Regulation of ISW2 by concerted action of  histone H4 tail and extranucleosomal DNA.
  31. Zofall, M, Persinger, J and Bartholomew, B.  (2004) Mol. Cell. Biol. 24, 11047-10057.  Functional role of extranucleosomal DNA and the entry site of the nucleosome in chromatin remodeling by ISW2.
  32. Kagalwala MN, Glaus BJ,  Dang, W.,  Zofall M, and Bartholomew B.  (2004) EMBO J .  23 (10), 2092-2104. Topography of the ISW2-Nucleosome Complex: Insights into the Mechanism of ATP-dependent Chromatin Remodeling by ISW2.  
  33. Auty R, Steen H, Myers LC, Persinger J, Bartholomew B, Gygi SP, Buratowski S. (2004) J. Biol. Chem. 279, 49973-81.  Purification of active TFIID from Saccharomyces cerevisiae. Extensive promoter contacts and co-activator function.
  34. Kassabov, S.K., Zhang, B., Persinger, J., and Bartholomew, B.  (2003) Mol. Cell 11, 391-403.  SWI/SNF Unwraps, Slides and Rewraps the Nucleosome.
  35. Vary JC Jr, Gangaraju VK, Qin J, Landel CC, Kooperberg C, Bartholomew B, Tsukiyama T. (2003) Mol. Cell. Biol. 23, 80-91.  Yeast Isw1p forms two separable complexes in vivo.
  36. Kassabov, S.K., Henry, N.H., Zofall, M., Tsukiyama, T. and Bartholomew, B.  (2002) Mol. Cell. Biol.22, 7524-7534.  High-resolution Mapping of Changes in Histone-DNA Contacts of Nucleosomes Remodeled by ISW2
  37. Sengupta, S.M., VanKanegan, M., Persinger, J., Logie, C., Cairns, B.R. Peterson, C.L. and Bartholomew, B.  (2001) J. Biol. Chem. 276, 12636-12644. The Interactions of Yeast SWI/SNF and RSC with the Nucleosome Before and After Chromatin Remodeling
  38. Zofall, M. and Bartholomew, B. (2000) Nucleic Acids Res. 28, 4382-4390. Two Novel dATP Analogues for DNA Photoaffinity Labeling.
  39. Sengupta, S.M., Persinger, J., Bartholomew, B. and Peterson, C.L. (1999) Methods 19, 434-446 . Use of DNA photoaffinity labeling to study nucleosome remodeling by SWI/SNF.
  40. Persinger, J., Sengupta, S.M., and Bartholomew, B. (1999) Mol. Cell. Biol. 19, 5218-5234, Spatial Organization of the Core Region of Yeast TFIIIB-DNA Complexes.
  41. Michelson, R.J., Collard, M.W., Ziemba, A.J., Persinger, J., Bartholomew, B., and Huggenvik, J.I. (1999) J. Biol. Chem. 274, 30510-30519.  Nuclear DEAF-1 related (NUDR) Protein Contains a Novel DNA Binding Domain and Represses Transcription of the Heterogeneous Nuclear Ribonucleoprotein A2/B1 Promoter.”
  42. Tate, J.J., Persinger, J., and Bartholomew, B. (1998) Nucleic Acids Res 26, 1421-1426. Survey of four different photoreactive moieties for DNA photoaffinity labeling of yeast RNA polymerase III transcription complexes
  43. Radebaugh, C.A., Gong, X., Bartholomew, B. and Paule, M.R. (1997) J Biol Chem 272, 3141-3144. Identification of Previously Unrecognized Common Elements in Eukaryotic Promoters: a Ribosomal RNA Initiator Element for RNA Polymerase I.
  44. Persinger J and Bartholomew B (1996) J. Biol. Chem., 271, 33039-33046. Mapping the Contacts of Yeast TFIIIB and RNA Polymerase III at Various Distances from the Major Groove of DNA by DNA Photoaffinity Labeling.
  45. Pruss D, Bartholomew B, Persinger J, Hayes J, Arents G, Moudrianakis EN, and Wolffe AP (1996) Science 274, 614-617.   A new model for the nucleosome: a binding site for linker histones inside the DNA gyres.
  46. Powell, W., Bartholomew, B., and Rienes, D. (1996) J.Biol.Chem. 271, 22301-22304. Elongation Factor SII Contacts the 3' End of RNA in RNA Polymerase II Elongation Complex.
  47. Lannutti, B.J., Persinger, J. and Bartholomew, B. (1996) Biochemistry 35, 9821-9831. 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.
  48. Bartholomew, B., Tinker, R.L., Kassavetis, G.A., and Geiduschek, E.P. (1995) Methods Enzymol. 262, 729-753. Photochemical Cross-linking Assay for DNA Tracking by Replication Proteins.
  49. Bartholomew, B., Braun, B.R., Kassavetis, G.A., and Geiduschek, E.P. (1994) J.Biol.Chem. 269, 18090-18095. Probing Close DNA Contacts of RNA Polymerase III Transcription Complexes with the Photoactive Nucleoside 4-Thiodeoxythymidine
  50. Bartholomew, B., Durkovich, D., Kassavetis, G.A., and Geiduschek. E.P. (1993) Mol.Cell.Biol. 13, 942-952. Orientation and Topography of RNA Polymerase III in Transcription Complexes.
  51. Braun BR, Bartholomew B, Kassavetis GA, Geiduschek EP (1992) J Mol Biol 228(4), 1063-77. 35. Topography of transcription factor complexes on the Saccharomyces cerevisiae 5 S RNA gene.
  52. Bartholomew B, Kassavetis GA, Geiduschek EP (1991) Mol Cell Biol 11(10), 5181-9. 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.
  53. Kassavetis GA, Bartholomew B, Blanco JA, Johnson TE, Geiduschek EP (1991) Proc Natl Acad Sci USA 88(16), 7308-12. Two essential components of the Saccharomyces cerevisiae transcription factor TFIIIB: transcription and DNA binding properties.
  54. Bartholomew B, Kassavetis GA, Braun BR, Geiduschek EP. (1990) EMBO J. 9(7), 2197-205. The subunit structure of Saccharomyces cerevisiae transcription factor IIIC probed with a novel photocrosslinking reagent.
  55. Bartholomew B, Meares CF, Dahmus ME. (1990) J Biol Chem 265(7), 3731-7.  Photoaffinity labeling of RNA polymerase III transcription complexes by nascent RNA.
  56. Bartholomew B, Dahmus ME, Meares CF. (1986) J Biol Chem 261(30), 14226-31. RNA contacts subunits II0 and IIC in HeLa RNA polymerase II transcription complexes.

Chapters in Professional Books

  1. Olefumi, L and Bartholomew B. (2012) “Chromatin Remodeling” Encyclopedia of Genetics 2nd Edition.
  2. Sen, P. Chatterjee, N., and Bartholomew, B. (2011)  “SWI/SNF Chromatin Remodeling Complex” in Encyclopedia of Signaling Molecules, Springer Publishers.
  3. Persinger, J. and Bartholomew, B. (2009) edited by T. Moss and B. Leblanc in "DNA-Protein Interactions: Principles and Protocols" 3rd Edition.  Site-directed DNA Crosslinking of Large Multi-subunit Protein-DNA Complexes
  4. Chatterjee, N., Sen, P. and Bartholomew, B. (2008) “The SWI/SNF and RSC Nucleosome Remodeling Complexes” in Handbook of Cell Signaling, Publisher Elsevier Inc.
  5. Kassabov, S.K., and Bartholomew, B.  (2004) Methods Enzymol. 375, 193-211.  “Site-Directed Histone-DNA Contact mapping for Analysis of Nucleosome Dynamics  High-resolution Mapping of Changes in Histone-DNA Contacts of Nucleosomes Remodeled by ISW2”. In Chromatin and Chromatin Remodeling, Eds. C.D. Allis & C. Wu
  6. Persinger, J. and Bartholomew, B. (2000) edited by T. Moss in "Methods in Molecular Biology: Protein-DNA Interaction Protocols".  Site-specific DNA photoaffinity labeling of RNA polymerase III transcription complexes
  7. Kassavetis, G.A., Bardeleben, C., Bartholomew, B., Braun, B.R., Joazeiro, C.A., Pisano, M. and Geiduschek, E.P. (1994) edited by J.W. Conaway and R.C. Conaway, in "Transcription Mechanisms and Regulation" Raven Press, New York. Transcription by RNA Polymerase III

© 2014 The University of Texas MD Anderson Cancer Center