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
The regulatory mechanisms
of eukaryotic transcription and its coupling to DNA repair
The 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)
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
- 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.
- Sukesh R. Bhaumik (2006) Analysis of in vivo targets of transcriptional
activators by fluorescence resonance energy transfer. Methods
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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:
- 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.
- 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,
- 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.
- 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.
- 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.
- 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
- Geetha Durairaj, Pooja Garg, and Sukesh R. Bhaumik (2009) Nuclear export
of mRNA and its regulation by ubiquitylation. RNA Biology
- 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.
- 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,
- Shivani Malik, and Sukesh R. Bhaumik (2010) Mixed lineage leukemia: histone
H3 lysine 4 methyltransferases from yeast to human. FEBS Journal,
- 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.
- Sukesh R. Bhaumik (2011) Distinct regulatory mechanisms of eukaryotic
transcriptional activation by SAGA and TFIID. Biochim Biophys
Acta.-Gene Regulatory Mechanisms, 1809, 97-108.
- 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:
- Sarah Frankland-Searby, and Sukesh R. Bhaumik (2011) The 26S proteasome
complex: An attractive target for cancer therapy. Biochimica
et Biophysica Acta – Reviews on Cancer. [Epub ahead
of print, October].
- Bhawana Uprety, Shweta Lahudkar, Shivani Malik, and Sukesh R. Bhaumik
(2011) 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, [Epub ahead of print, November].
- Abhijit Shukla, Shweta Lahudkar, Geetha Durairaj, and Sukesh R. Bhaumik
(2011) Sgf29p facilitates the recruitment of TATA-box-binding protein, but
does not alter SAGA’s global structural integrity in vivo. Biochemistry,
[Epub ahead of print, December].
- Shivani Malik, Priyari Chaurasia, Shweta Lahudkar, Bhawana Uprety, and
Sukesh R. Bhaumik (2011) Rad26p regulates the occupancy of histone H2A-H2B
dimer at the active genes in vivo. Nucleic Acids Research.
(accepted for publication, November).
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