Sukesh R. Bhaumik

Professor and Distinguished Scholar

B. Sc. Ramakrishna Mission Residential College, Narendrapur (University of Calcutta),1990; M. Sc. Indian Institute of Technology, Bombay, 1992; Ph. D. Tata Institute of Fundamental Research, Bombay, 1997; Postdoctoral Fellow, Howard Hughes Medical Institute at the University of Massachusetts Medical School, 1998-2003; Appointed as faculty, Dept. of Biochemistry & Molecular Biology, SIUC, 2003-present.

phone: (618) 453-6479
email: sbhaumik@siumed.edu

Regulatory mechanisms of eukaryotic transcription and its coupling to DNA repair

Research in my laboratory is focused on understanding the regulatory mechanisms of eukaryotic transcription and its coupling to DNA repair. Transcription is regulated by the 26S proteasome complex. However, the precise mechanisms of gene regulation by the proteasome complex are not clearly understood. Understanding the regulatory mechanisms of gene expression by the proteasome complex is crucial for designing better therapeutic agents to maintain normal cellular functions, since a growing number of human diseases are linked to the proteasome complex. Thus, we are carrying out the experiments to understand the mechanisms-of-action of the proteasome complex in regulation of eukaryotic transcription. Intriguingly, transcription is also coupled to DNA repair, and such a repair mode is referred to as transcription-coupled repair (TCR). TCR specifically removes lesions from the body of the active gene. Various types of cancers and other human diseases are predisposed by the defects in the TCR process. Therefore, it is essential to understand the regulatory mechanisms of TCR for possible cures of a number of human diseases. However, the molecular regulatory mechanisms of TCR have remained elusive despite the fact that the process was discovered two decades ago. Thus, we are carrying out the experiments to determine the cellular mechanisms that couple transcription to genome integrity in living eukaryotic cells.

Recent Publications (2006-present)

  1. Abhijit Shukla, Nadia Stanojevic, Zhen Duan, Payel Sen and Sukesh R. Bhaumik (2006) Ubp8p, a histone deubiquitinase whose association with SAGA is mediated by Sgf11p, differentially regulates lysine 4 methylation of histone H3 in vivo. Molecular and Cellular Biology 26: 3339-3352.
  1. Abhijit Shukla, Nadia Stanojevic, Zhen Duan, Thomas Shadle and Sukesh R. Bhaumik (2006) Functional analysis of H2B-K123 ubiquitination in regulation of H3-K4 methylation and recruitment of RNA polymerase II at the coding sequences of several active genes in vivo. Journal of Biological Chemistry 281: 19045-19054.
  1. Sukesh R. Bhaumik (2006) Analysis of in vivo targets of transcriptional activators by fluorescence resonance energy transfer. Methods 40: 353-350.
  1. Abhijit Shukla, Pratibha Bajwa and Sukesh R. Bhaumik (2006) SAGA-associated Sgf73p facilitates formation of the preinitiation complex assembly at the promoters either in a HAT-dependent or independent manner in vivo. Nucleic Acids Research 34: 6225-6232.
  1. Jessica Schneider, Pratibha Bajwa, Farley C. Johnson, Sukesh R. Bhaumik and Ali Shilatifard (2006) Rtt109 is required for proper H3K56 acetylation: A chromatin mark associated with the elongating RNA polymerase II. Journal of Biological Chemistry 281: 37270-37274.
  1. Adam Wood, Abhijit Shukla, Jessica Schneider, Jung Shin Lee, Julie D. Stanton, Tiffany Dzuiba, Selene K. Swanson, Laurence Florens, Michael P. Washburn, John Wyrick, Sukesh R. Bhaumik and Ali Shilatifard (2007) Ctk complex regulation of histone methylation by COMPASS. Molecular and Cellular Biology 27: 709-720.
  1. Abhijit Shukla and Sukesh R. Bhaumik (2007) H2B-K123 ubiquitination stimulates RNAPII elongation independent of H3-K4 methylation. Biochemical and Biophysical Research Communications 359: 214-220.
  1. Sukesh R. Bhaumik, Edwin Smith, and Ali Shilatifard (2007) Histone covalent modifications in development and disease pathogenesis. Nature Structural and Molecular Biology 14: 1008-1016.
  1. Jung-Shin Lee, Abhijit Shukla, Jessica Schneider, Laurence Florens, Selene K. Swanson, Michael P. Washburn, Sukesh R. Bhaumik and Ali Shilatifard (2007) Translating histone crosstalk between H2B monoubiquitination and H3 methylation by COMPASS and Dot1. Cell 131: 1084-1096.
  1. Shivani Malik, Shruti Bagla, Priyasri Chaurasia, Zhen Duan, and Sukesh R. Bhaumik (2008) Elongating RNA polymerase II is disassembled through specific degradation of its largest but not other subunits in response to DNA damage in vivo. Journal of Biological Chemistry 283: 6897-905.
  1. Sukesh R. Bhaumik, and Shivani Malik (2008) Diverse regulatory mechanisms of eukaryotic transcriptional activation by the proteasome complex. Critical Reviews in Biochemistry and Molecular Biololgy 43: 419-33.
  1. Abhijit Shukla, Priyasri Chaurasia, and Sukesh R. Bhaumik (2009) Histone methylation and ubiquitination with their cross-talk and roles in gene expression and stability. Cellular and Molecular Life Sciences, 66: 1419-33.
  1. Song Qin, Qien Wang, Alo Ray, Gulzar Wani, Qun Zhao, Sukesh R. Bhaumik, and Altaf A. Wani (2009) Sem1p and Ubp6p orchestrate telomeric silencing by modulating histone H2B ubiquitination and H3 acetylation. Nucleic Acids Research, 37: 1843-53.
  1. Abhijit Shukla, Aparna Natarajan, Sukesh R. Bhaumik, Hany El Shemy, and David Lightfoot (2009) The interactions of the largest subunit of RNA polymerase II with other cellular proteins: a bioinformatic approach. Current Issues in Molecular Biology, 11: i65-71.
  1. Tej K. Pandita, Shruti Pandita, and Sukesh R. Bhaumik (2009) Molecular parameters of hyperthermia for radiosensitization. Critical Reviews in Eukaryotic Gene Expression, 19: 235-51.
  1. Abhijit Shukla, Geetha Durairaj, Jessica Schneider, Zhen Duan, Thomas Shadle, and Sukesh R. Bhaumik (2009) Stimulation of mRNA export by an F-box protein, Mdm30p, in vivo. Journal of Molecular Biology 389, 238-47.
  1. Geetha Durairaj, Pooja Garg, and Sukesh R. Bhaumik (2009) Nuclear export of mRNA and its regulation by ubiquitylation. RNA Biology 6, 531-5.
  1. Shivani Malik, Abhijit Shukla, Payel Sen, and Sukesh R. Bhaumik (2009) The 19S proteasome subcomplex establishes a specific protein interaction network at the promoter for stimulated transcriptional initiation in vivo. Journal of Biological Chemistry 284, 35714-24.
  1. Shivani Malik, Priyasri Chaurasia, Shweta Lahudkar, Geetha Durairaj, Abhijit Shukla, and Sukesh R. Bhaumik (2010) Rad26p, a transcription-coupled repair factor, is recruited to the site of DNA lesion in an elongating RNA polymerase II-dependent manner in vivo. Nucleic Acids Research, 38, 1461-77.
  1. Shivani Malik, and Sukesh R. Bhaumik (2010) Mixed lineage leukemia: histone H3 lysine 4 methyltransferases from yeast to human. FEBS Journal, 277, 1805-21.
  1. Geetha Durairaj, Priyasri Chaurasia, Shweta Lahudkar, Shivani Malik, Abhijit Shukla, and Sukesh R. Bhaumik (2010) Regulation of chromatin assembly/disassembly by Rtt109p, a histone H3 Lys56-specific acetyltransferase, in vivo. Journal of Biological Chemistry, 285, 30472-9.
  1. Sukesh R. Bhaumik (2011) Distinct regulatory mechanisms of eukaryotic transcriptional activation by SAGA and TFIID. Biochim Biophys Acta.-Gene Regulatory Mechanisms, 1809, 97-108.
  1. Shweta Lahudkar, Abhijit Shukla, Pratibha Bajwa, Geetha Durairaj, Nadia Stanojevic, and Sukesh R. Bhaumik (2011) The mRNA cap-binding complex stimulates the formation of pre-initiation complex at the promoter via its interaction with Mot1p in vivo. Nucleic Acids Research, 39: 2188-2209.
  1. Shivani Malik, Sukesh R. Bhaumik, and David A. Lightfoot (2012) Review of the Rpt3 genes encoding part of the 26S proteasome associated with loci underlying disease resistance in soybean. Atlas Journal of Biology, 2, 88-93.
  1. Sarah Frankland-Searby, and Sukesh R. Bhaumik (2012) The 26S proteasome complex: An attractive target for cancer therapy. Biochimica et Biophysica Acta – Reviews on Cancer, 1825: 64-76.
  1. Bhawana Uprety, Shweta Lahudkar, Shivani Malik, and Sukesh R. Bhaumik (2012) The 19S proteasome subcomplex promotes the targeting of NuA4 HAT to the promoters of ribosomal protein genes to facilitate the recruitment of TFIID for transcriptional initiation in vivo. Nucleic Acids Research, 40:1969-83.
  1. Abhijit Shukla, Shweta Lahudkar, Geetha Durairaj, and Sukesh R. Bhaumik (2012) Sgf29p facilitates the recruitment of TATA-box-binding protein, but does not alter SAGA’s global structural integrity in vivo. Biochemistry, 51:706-14.
  1. Shivani Malik, Priyari Chaurasia, Shweta Lahudkar, Bhawana Uprety, and Sukesh R. Bhaumik (2012) Rad26p regulates the occupancy of histone H2A-H2B dimer at the active genes in vivo. Nucleic Acids Research, 40, 3348-63.
  1. Shivani Malik and Sukesh R. Bhaumik (2012) Rad26p, a transcription-coupled repair factor, promotes the eviction and prevents the reassociation of histone H2A-H2B dimer during transcriptional elongation in vivo. Biochemistry, 51: 5873-5.
  1. Priyasri Chaurasia, Rwik Sen, Tej K. Pandita, and Sukesh R. Bhaumik (2012) Preferential DNA double-strand break repair at the active gene. Journal of Biological Chemistry, 287: 36414-22.
  1. Priyasri Chaurasia, Rwik Sen, and Sukesh R. Bhaumik (2013) Functional analysis of Rad14p, a DNA damage recognition factor in nucleotide excision repair, in regulation of transcription in vivo. Journal of Biological Chemistry, 288: 793-806.
  1. Rwik Sen, Shweta Lahudkar, Geetha Durairaj, and Sukesh R. Bhaumik (2013) Functional analysis of Bre1p, an E3 ligase for histone H2B ubiquitylation, in regulation of RNA polymerase II association with active genes and transcription in vivo. Journal of Biological Chemistry, 288: 9619-33.
  1. Shivani Malik, Geetha Durairaj, and Sukesh R. Bhaumik (2013) Mechanisms of antisense transcription initiation from the 3’-end of the GAL10 coding sequence in vivo. Molecular and Cellular Biology, 33: 3549-67.
  1. Rwik Sen, and Sukesh R. Bhaumik (2013) Transcriptional stimulatory and repressive functions of histone H2B ubiquitin ligase. Transcription, 4: 221-6.
  1. Shweta Lahudkar, Geetha Durairaj, Bhawana Uprety, and Sukesh R. Bhaumik (2014) A novel role for Cet1p mRNA 5'-triphosphatase in promoter proximal accumulation of RNA polymerase II in Saccharomyces cerevisiae. Genetics, 196:161-76.
  1. Geetha Durairaj, Shweta Lahudkar, and Sukesh R. Bhaumik (2014) A new regulatory pathway of mRNA export by an F-box protein, Mdm30. RNA, 20:133-42.
  1. Geetha Durairaj, Rwik Sen, Bhawana Uprety, Abhijit Shukla, and Sukesh R. Bhaumik. (2014) Sus1p facilitates pre-initiation complex formation at the SAGA-regulated genes independently of histone H2B de-ubiquitylation. Journal Molecular Biology, 426: 2928-41.
  1. Rwik Sen, Shivani Malik, Sarah Frankland-Searby, Bhawana Uprety, Shweta Lahudkar, and Sukesh R. Bhaumik (2014) Rrd1p, an RNA polymerase II-specific prolyl isomerase and activator of phosphoprotein phosphatase, promotes transcription independently of rapamycin response. Nucleic Acids Research, 42: 9892-907.
  1. Shivani Malik and Sukesh R. Bhaumik (2014) Regulation of active genome integrity and expression. Nucleus, 5: 520-6.
  1. Bhawana Uprety, Rwik Sen, and Sukesh R. Bhaumik (2015) Eaf1p is required for recruitment of NuA4 in targeting TFIID to the promoters of the ribosomal protein genes for transcriptional initiation in vivo. Molecular and Cellular Biology,35:2947-64.
  1. Geetha Durairaj, Sukesh R. Bhaumik, and David A. Lightfoot (2016) The life of mRNA and its genome-wide analysis. Trends in Cell and Molecular Biology, 11, 35-40.
  1. Bhawana Uprety, Amala Kaja, Jannatul Ferdoush, Rwik Sen, and Sukesh R. Bhaumik (2016) Regulation of antisense transcription by NuA4 histone acetyltransferase and other chromatin regulatory factors. Molecular and Cellular Biology, 36: 992-1006.
  1. Rwik Sen, Jannatul Ferdoush, Amala Kaja, and Sukesh R. Bhaumik (2016) Fine-tuning of FACT by ubiquitin proteasome system in regulation of transcriptional elongation. Molecular and Cellular Biology, 36:1691-703.
  1. Geetha Durairaj, Shivani Malik, and Sukesh R. Bhaumik (2017) Regulatory mechanisms of eukaryotic gene expression. Gene regulation, Epigenetics and Hormone Signaling (Editor: S. Mandal). Wiley-VCH, Germany. Volume 1, 1-28.
  1. Jannatul Ferdoush, Saswati Karmakar, Priyanka Barman, Amala Kaja, Bhawana Uprety, Surinder K. Batra, and Sukesh R. Bhaumik (2017) Ubiquitin-Proteasome System Regulation of an Evolutionarily Conserved RNA Polymerase II-Associated Factor 1 Involved in Pancreatic Oncogenesis. Biochemistry, 56, 6083-6086.
  1. Rwik Sen, Amala Kaja, Jannatul Ferdoush, Shweta Lahudkar, Priyanka Barman, and Sukesh R. Bhaumik (2017) An mRNA capping enzyme targets FACT to the active gene to enhance the engagement of RNA polymerase II into transcriptional elongation. Molecular and Cellular Biology, 37: e00029-17.
  1. Jannatul Ferdoush, Rwik Sen, Amala Kaja, Priyanka Barman, and Sukesh R. Bhaumik (2018) Two Distinct Regulatory Mechanisms of Transcriptional Initiation in Response to Nutrient Signaling. Genetics, 208, 191-205.
  1. Saswati Karmakar, Parama Dey, Arokia P. Vaz, Sukesh R. Bhaumimk, Moorthy P. Ponnusamy, and Surinder K. Batra (2018) PD2/PAF1 at the crossroads of the cancer network. Cancer Research, 78, 313-319.
  1. Bhawana Uprety, Amala Kaja, and Sukesh R. Bhaumik (2018) TOR facilitates the targeting of the 19S proteasome subcomplex to enhance transcription complex assembly at the promoters of the ribosomal protein genes. Molecular and Cellular Biology, 38, pii: e00469-17.
  1. Saswati Karmakar, Moorthy P Ponnusamy, Sukesh R. Bhaumik, and Surinder K. Batra (2018) RNA polymerase II and associated transcription factors. Encyclopedia in Life Science (eLS). John Wiley & Sons, Ltd., Chichester.
  1. Priyanka Barman, Divya Reddy, and Sukesh R. Bhaumik (2019) Mechanisms of antisense transcription initiation with implications in gene expression, genomic integrity and disease pathogenesis. Non-coding RNA, 5, pii: E11.
  1. Rwik Sen, Priyanka Barman, Amala Kaja, Jannatul Ferdoush, Shweta Lahudkar, and Sukesh R. Bhaumik (2019) Distinct functions of the cap-binding complex in stimulation of nuclear mRNA export. Molecular and Cellular Biology, 39, pii: e00540-18.

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