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Fields
- Gene
Expression
- Chromatin
- Yeast
Genetics
Research
Description
Our
laboratory studies the regulation of gene expression in
eukaryotic organisms. We are especially interested in transcription
of protein-encoding genes by RNA polymerase II (Pol II).
The experimental organism used in most of our work
is the yeast Saccharomyces cerevisiae , which enables
us to use a powerful combination of classical genetics,
molecular biology and modern biochemistry in our research.
Our current efforts are focused on two questions:
1) How is the transcription coupled to RNA processing?
and 2) How do gene loops that juxtapose the 3'-end of the
gene with the promoter affect the mechanism and regulation
of gene expression?
1)
Coupling of 3' end processing to Pol II transcription.
Nascent mRNA undergoes modifications that include 5' capping,
splicing, 3' endonucleolytic cleavage and polyadenylation.
These processing events occur co-transcriptionally
and involve recruitment and exchange of processing enzymes
to the C-terminal domain (CTD) of the Rpb1 subunit of Pol
II. The CTD is phosphorylated and dephosphorylated
at Ser2 and Ser5 during the transcription cycle.
We recently discovered that the Ssu72 protein is an integral
component of the CPF 3' end processing complex and is a
CTD Ser5-P phosphatase. We are now focused on (i)
determining how Ssu72-mediated Ser5-P dephosphorylation
affects Pol II progression through the transcription cycle;
(ii) how Ssu72 is regulated by the transcriptional machinery;
and (iii) how Ssu72 is regulated by 3' end processing factors.
These questions are being addressed in collaboration
with Professor Claire Moore ( Tufts Medical School ).
2)
Role of “gene loops” in transcription. Although
Ssu72 is a component of the CPF 3' end processing complex,
we first identified this protein based on genetic and physical
interactions with TFIIB, a transcription initiation factor.
As such, Ssu72 defined an unexpected link between
the Pol II initiation and termination machineries.
This suggested to us that the ends of gene might physically
interact to form gene loops. Our recent studies revealed
that gene loops are a general feature of Pol II transcription.
Looping is dependent upon transcription and requires specific
components of the transcription initiation and 3'-end processing
complexes, including the Ssu72 CTD phosphatase. We are now
working (i) to define the factors and mechanisms involved
in loop formation; and (ii) to determine the functional
significance of gene loops with respect to regulation of
gene expression.
A
remarkable feature of Pol II transcription and mRNA processing
is the extent to which these two coupled processes – and
the proteins that facilitate them – are conserved among
eukaryotic organisms. Accordingly, we are able to
exploit the extensive arsenal of experimental approaches
available in yeast with the results directly applicable
to human biology and medicine.
Selected
Publications:
LAINÉ, J.-P., B.N. SINGH, S. KRISHNAMURTHY and M. HAMPSEY (2009) A physiological role for gene loops in yeast. Genes & Dev. 23: 2604-2609.
KRISHNAMURTHY, S. and M. HAMPSEY (2009) Eukaryotic transcription initiation. Curr. Biol. 19:R153-R156
GHAZY, M., X. HE, B.N. SINGH, M. HAMPSEY and C. MOORE (2009) The essential N-terminus of the Pta1 scaffold protein is required for snoRNA transcription termination and Ssu72 function but is dispensable for pre-mRNA 3’-end processing. Mol. Cell. Biol. 29: 2296-2307.
KRISHNAMURTHY, S., M. A. GHAZY, C. MOORE and M. HAMPSEY (2009) Functional interaction of the Ess1 prolyl isomerase with components of the RNA polymerase II initiation and termination machineries. Mol. Cell. Biol. 29:2925-2934.
SINGH, B.N., A. ANSARI and M. HAMPSEY (2009) Detection of transient short-range chromatin interactions by 3C in yeast. Methods 48:361-367.
ESTRELLA,
L. A., S. KRISHNAMURTHY, C. R. TIMME and M. HAMPSEY (2008)
The Rsp5 E3 ligase mediates turnover of low-affinity phosphate
transporters in Saccharomyces cerevisiae. J.
Biol. Chem. 283:5327-5334.
SINGH,
B. N. and M. HAMPSEY (2007) A transcription-independent
role for TFIIB in gene looping. Mol. Cell
27:806-816.
REYES-REYES,
M. and M. HAMPSEY (2007) Role for the Ssu72 C-terminal domain
phosphatase in RNA polymerase II transcription elongation.
Mol. Cell. Biol. 27:926-936.
HAMPSEY,
M. (2006) The RNA polymerase II initiation complex: looking
for a place to start. Nat. Struct. Mol. Biol. 13
:564-566.
ANSARI,
A. and M. HAMPSEY (2005) A role for the CPF 3'-end processing
machinery in RNAP II-dependent gene looping. Genes
& Dev. 19 :2969-2978.
KRISHNAMURTHY,
S., X. HE, M. REYES-REYES, C. MOORE AND M. HAMPSEY (2004)
Ssu72 is a RNA polymerase II CTD phosphatase. Mol.
Cell 14 :387-394.
CHEN,
B.-S. and M. HAMPSEY (2004) Functional interaction between
TFIIB and the Rpb2 subunit of RNA polymerase II: implications
for the mechanism of transcription start site selection.
Mol. Cell Biol. 24 :3983-3991.
HAMPSEY,
M. and D. REINBERG (2003) Tails of intrigue: phosphorylation
of RNA polymerase II mediates histone methylation. Cell
113 :429-432.
HE,
X., A.U. KHAN, H. CHENG, D.L. PAPPAS, M. HAMPSEY and
C.L. MOORE (2003) Functional interactions
between the transcription and mRNA 3' end processing machineries
mediated by Ssu72 and Sub1. Genes & Dev. 17
:1030-1042.
WOYCHIK,
N.A. and M. HAMPSEY (2002) The RNA polymerase
II machinery: structure illuminates function. Cell
108 :453-463.
Laboratory
Personnel :
Adjunct
Assistant Professor
- Krishnamurthy
Shankarling, PhD
Postdoctoral
Fellow:
Graduate
Students:
- Shivani
Goel , MS
- Jesus
Rosado, BS
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Postdoctoral Fellows/Graduate Students/Research Technicians:
Athar
Ansari, Ph.D., adjunct assistant professor
Jean-Philippe
Lainé, Ph.D., postdoctoral fellow
Mariela
Reyes-Reyes, Ph.D., 2006, graduate student
Luis
A. Estrella, Ph.D., 2004, graduate student
Asad
U. Khan, Ph.D., postdoctoral fellow
Bo-Shiun
Chen, Ph.D., 2003, graduate student
Wei-Hua
Wu, Ph.D., 2001, graduate student
M.
Angeles Freire-Picos, Ph.D., postdoctoral fellow; visiting
professor
Amy
Tessmer Pappas, research techician
Donald
L. Pappas, Jr., Ph.D., 2000, graduate student
Zu-Wen
Sun, Ph.D., 1996, graduate student, postdoctoral fellow
Rhonda
W. Berroteran, Ph.D., 1995, research tech., graduate student
Katy
O'Mara, research technician
Dan
E. Ware, M.S., M.D., 1991, graduate student
Jong
G. Na, Ph.D., 1992, graduate student
Inés
Pinto, Ph.D., 1992, graduate student
Former
Undergraduate Students:
Lori Russo, B.S., medical student (RWJMS)
Sophia
Sequeira, undergraduate student (Williams College)
Cindy
R. Timme, B.S., undergraduate student (Rutgers)
Dianaliz
Santiago, B.S., (Univ. Puerto Rico - Mayagüez)
Mark
Neurohr-Pierpaoli, B.S., undergraduate student (Rutgers)
Jin
Cho, B.S., undergraduate student (Rutgers)
Ashis
Bhutani, B.S., undergraduate student (Rutgers)
Alexandra
Terskiy, B.S., undergraduate student (Rutgers)
Francia
Francis, B.S., undergraduate student (Rutgers)
Annette
Seda, undergraduate student (Univ. Puerto Rico - Mayagüez)
Dimple
Patel, B.S., undergraduate student (Rutgers)
Taly
Garcia-Muñiz, B.S., undergraduate student (Rutgers)
Vimal
Patel, B.S., undergraduate student (Rutgers)
Sonal
Patel, B.S., undergraduate student (Rutgers)
Rajan
Mitchell, B.S., undergraduate student (Rutgers)
Mary
Mai, B.S., undergraduate student (Rutgers)
Jeffrey
Beasley, high school student (Louisiana)
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