Despite the availability of precise consensus DMA-binding sequences for hundreds of proteins, and the complete genome sequence of dozens of organisms, it is not possible to predict where a given DNA-binding protein will associate with a genome in vivo. How DNA-binding proteins recognize and bind to a subset of genomic DNA sequences, while at the same time not binding to thousands of computationally indistinguishable sequences, remains a major unsolved problem in biology. Using Saccharomyces cerevisiae as a model system, we have developed a unique set of genetic, biochemical, and genomic tools to attack this problem. .
Aim one : Our previous work has shown that in vivo, transcription factors bind to DNA upstream of genes in preference to coding regions, even though both regions contain strong consensus binding sites. Cooperative protein-protein-DNA interactions and differential chromatin accessibility are hypothesized to mediate context-dependent binding. To quantitate the degree of specificity dependent on in vivo factors, and how much is inherent to the protein and DNA, the genome-wide specificities of Raplp and LeuSp will be determined in vitro using purified proteins and naked yeast genomic DNA, and compared to specificity in vivo. Changes in the distribution of Raplp in response to changes in environmental conditions will also be determined.
Aim two : Our previous work has shown that nucleosome occupancy throughout the genome is heterogeneous in living yeast cells. We propose experiments to determine the molecular basis for differential nucleosome occupancy, and how it is established, regulated, and maintained in yeast.
Aim three : Our data and data from other groups suggest an intimate relationship between target selection by DMA binding proteins (addressed in Aim 1), global chromatin organization (addressed in Aim 2), and transcriptional activity.
The third aim specifically tests relationships between these three processes. We will assay Rap1p target selection in strains in which (i) the context of Raplp binding sites has been changed (ii) transcription at specific loci has been disabled, and (iii) the RNA Pol II CTD is mutated. We will map transcription-coupled chromatin modifications and perform high-throughput site-directed mutagenesis to link histone structure and modification to biological outcomes. Human Health: Transcription factors, when missexpressed or mutated, are a prevalent cause of human disease. Better prediction of their in vivo targets may lead to therapies that inhibit binding to inappropriate targets. FAIRE, a new chromatin assay we have developed, has potential as a prognostic or diagnostic tool for diseases (including cancer) that affect, or arise from defects in, chromatin or transcription.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM072518-03
Application #
7262468
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Carter, Anthony D
Project Start
2005-08-01
Project End
2010-07-31
Budget Start
2007-08-01
Budget End
2008-07-31
Support Year
3
Fiscal Year
2007
Total Cost
$266,486
Indirect Cost
Name
University of North Carolina Chapel Hill
Department
Genetics
Type
Schools of Medicine
DUNS #
608195277
City
Chapel Hill
State
NC
Country
United States
Zip Code
27599
Lickwar, Colin R; Mueller, Florian; Lieb, Jason D (2013) Genome-wide measurement of protein-DNA binding dynamics using competition ChIP. Nat Protoc 8:1337-53
Grohman, Jacob K; Gorelick, Robert J; Lickwar, Colin R et al. (2013) A guanosine-centric mechanism for RNA chaperone function. Science 340:190-5
Lickwar, Colin R; Mueller, Florian; Hanlon, Sean E et al. (2012) Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature 484:251-5
Gossett, Andrea J; Lieb, Jason D (2012) In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. PLoS Genet 8:e1002771
Hanlon, Sean E; Rizzo, Jason M; Tatomer, Deirdre C et al. (2011) The stress response factors Yap6, Cin5, Phd1, and Skn7 direct targeting of the conserved co-repressor Tup1-Ssn6 in S. cerevisiae. PLoS One 6:e19060
Lickwar, Colin R; Rao, Bhargavi; Shabalin, Andrey A et al. (2009) The Set2/Rpd3S pathway suppresses cryptic transcription without regard to gene length or transcription frequency. PLoS One 4:e4886
Kaplan, Noam; Moore, Irene K; Fondufe-Mittendorf, Yvonne et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458:362-6
Field, Yair; Fondufe-Mittendorf, Yvonne; Moore, Irene K et al. (2009) Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nat Genet 41:438-45
Berchowitz, Luke E; Hanlon, Sean E; Lieb, Jason D et al. (2009) A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae. Genome Res 19:2245-57
Giresi, Paul G; Lieb, Jason D (2009) Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods 48:233-9

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