The DMA in the chromatin of a eukaryotic cell is highly packed and yet the information contained in the DNA must be made accessible, in a regulated way, to the cellular machinery that decodes it to make the proteins that are the main catalytic and structural components of the cell. The first step in this decoding process, transcription, is carried out by RNA polymerase which functions as a highly processive molecular motor that moves along the DNA template transcribing genetic information from DNA to messenger RNA. During transcription, RNA polymerase and other transcription factors must be able to access the DNA that is packed into nucleosomes and transcription is in part regulated by the accessibility of the DNA. Transcription in chromatin and its regulation must necessarily be highly kinetic processes involving directed molecular motions. Therefore, the long-term goals of our research are to understand on a kinetic and mechanical level (1) the many processes by which the DNA that is packed in nucleosomes is made accessible to RNA polymerase and other transcription factors, (2) how various RNA polymerases transcribe nucleosomal DNA, and (3) the functioning of the regulatory factors involved in these processes. In this project, we propose to use novel and powerful single molecule biophysical approaches that have been recently developed in the Pi's lab to make direct measurements of some of these molecular events.
The specific aims of this proposal focus on the effects of chromatin remodeling machines on nucleosomal stability and DNA accessibility, how RNA polymerase overcomes the nucleosome obstacle, and the effects of transcription on nucleosomes. We expect our studies to make significant contributions to the understanding of transcription and its regulation in chromatin.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM059849-09
Application #
7410172
Study Section
Special Emphasis Panel (ZRG1-MGA (01))
Program Officer
Lewis, Catherine D
Project Start
1999-07-01
Project End
2012-03-31
Budget Start
2008-04-01
Budget End
2012-03-31
Support Year
9
Fiscal Year
2008
Total Cost
$272,736
Indirect Cost
Name
Cornell University
Department
Physics
Type
Schools of Arts and Sciences
DUNS #
872612445
City
Ithaca
State
NY
Country
United States
Zip Code
14850
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Nodelman, Ilana M; Horvath, Kyle C; Levendosky, Robert F et al. (2016) The Chd1 chromatin remodeler can sense both entry and exit sides of the nucleosome. Nucleic Acids Res 44:7580-91
Sun, Bo; Pandey, Manjula; Inman, James T et al. (2015) T7 replisome directly overcomes DNA damage. Nat Commun 6:10260
Li, Ming; Hada, Arjan; Sen, Payel et al. (2015) Dynamic regulation of transcription factors by nucleosome remodeling. Elife 4:
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Brennan, Lucy D; Roland, Thibault; Morton, Diane G et al. (2013) Small molecule injection into single-cell C. elegans embryos via carbon-reinforced nanopipettes. PLoS One 8:e75712
Sheinin, Maxim Y; Li, Ming; Soltani, Mohammad et al. (2013) Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss. Nat Commun 4:2579
Dame, Remus T; Hall, Michael A; Wang, Michelle D (2013) Single-molecule unzipping force analysis of HU-DNA complexes. Chembiochem 14:1954-7
Ma, Jie; Bai, Lu; Wang, Michelle D (2013) Transcription under torsion. Science 340:1580-3

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