Analysis of genome-wide transcriptional control in yeast The long term goal of this project is to develop a comprehensive and predictive model of a functional transcriptional regulatory network in a eukaryotic cell. We seek to understand genome-wide transcriptional changes that are triggered in response to stress conditions, in terms of the quantitative contributions of individual transcriptional regulators, including sequence-specific DNA binding transcription factors as well as transcriptional regulators that affect gene expression through modulating chromatin structure. We will use yeast as a model system to address several questions in this area through the following specific aims. First, we will comprehensively identify every transcriptional regulator and chromatin factor that potentially regulates stress responses in yeast. This will be accomplished through phenotypic growth assays of yeast strains in which transcription factor function is modulated by deletion or overexpression. Transcription factor deletion and overexpression strains will be screened for growth defects by spotting on plates and growth in liquid, under three different stress conditions - heat shock, nutrient starvation and DNA damage. Second, we will identify the downstream targets of key regulators under stress conditions. We will identify the direct binding targets of a prioritized set of transcription regulators during the stress responses that they are shown to be required for, using chromatin immunoprecipitation combined with microarrays (ChIP-chip). We will also identify the genes that are actively and functionally regulated by these factors, by carrying out gene expression profiling in strains deleted for the selected transcription factors, under the stress conditions that these factors are known to be required for. Finally, we will integrate our experimental genomic data to build a predictive and causal regulatory network to explain the transcriptional regulation of all yeast genes under stress. We will use a Bayesian framework to model and reconstruct this transcriptional regulatory network, which will minimally contain the targets of every stress-related transcriptional regulator in yeast, and ideally explain the regulation of every yeast gene under physiological stress perturbations. We will test the predictive ability of our network using both external experimental data and gene functional annotations. Selected predicted regulatory relationships in the network will be verified by directed experiments.

Public Health Relevance

Analysis of genome-wide transcriptional control in yeast This project will use the stress response in yeast as a model system to understand the global regulation of gene expression under physiological perturbation. Homologs of many of the transcriptional regulators active during this process in yeast, such as Heat Shock Factor and other factors that affect chromatin are directly implicated in cancer in mammalian cells. A global functional gene regulatory network such as we propose to construct will shed considerable light on the mechanism of global gene regulation in mammalian cells that is often impaired in disease.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA095548-09
Application #
8208192
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Li, Jerry
Project Start
2002-04-01
Project End
2014-01-31
Budget Start
2012-02-01
Budget End
2013-01-31
Support Year
9
Fiscal Year
2012
Total Cost
$255,793
Indirect Cost
$81,011
Name
University of Texas Austin
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
170230239
City
Austin
State
TX
Country
United States
Zip Code
78712
Bagchi, Dia N; Iyer, Vishwanath R (2016) The Determinants of Directionality in Transcriptional Initiation. Trends Genet 32:322-33
Dekker, Joseph D; Park, Daechan; Shaffer 3rd, Arthur L et al. (2016) Subtype-specific addiction of the activated B-cell subset of diffuse large B-cell lymphoma to FOXP1. Proc Natl Acad Sci U S A 113:E577-86
Zhang, Dingxiao; Park, Daechan; Zhong, Yi et al. (2016) Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer. Nat Commun 7:10798
Park, Daechan; Shivram, Haridha; Iyer, Vishwanath R (2014) Chd1 co-localizes with early transcription elongation factors independently of H3K36 methylation and releases stalled RNA polymerase II at introns. Epigenetics Chromatin 7:32
Park, Daechan; Morris, Adam R; Battenhouse, Anna et al. (2014) Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements. Nucleic Acids Res 42:3736-49
Park, Daechan; Lee, Yaelim; Bhupindersingh, Gurvani et al. (2013) Widespread misinterpretable ChIP-seq bias in yeast. PLoS One 8:e83506
Iyer, Vishwanath R (2012) Nucleosome positioning: bringing order to the eukaryotic genome. Trends Cell Biol 22:250-6
Lee, Bum-Kyu; Iyer, Vishwanath R (2012) Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation. J Biol Chem 287:30906-13
Shivaswamy, Sushma; Iyer, Vishwanath R (2008) Stress-dependent dynamics of global chromatin remodeling in yeast: dual role for SWI/SNF in the heat shock stress response. Mol Cell Biol 28:2221-34
Shivaswamy, Sushma; Iyer, Vishwanath R (2007) Genome-wide analysis of chromatin status using tiling microarrays. Methods 41:304-11

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