The regulation of eukaryotic genes involves many hundreds of proteins. How they work together at the many thousands of genes that comprise a genome is not known. Little is known about how this interplay changes as cellular genomes are reprogrammed in response to signaling events such as environmental stress. The work proposed here is a continuation of a project to broadly survey where transcriptional regulatory proteins are located throughout the genome of the model eukaryotic organism Saccharomcyes cerevisiae, and where they translocate to when the genome is reprogrammed by environmental signals, such as heat shock and other stresses. Heat shock provides a rapid and simple programming event for the cell. Current studies on this project have already revealed novel insights into gene regulation by demonstrating that pre-initiation complexes partially assemble in nucleosome-free promoter regions. However, full assembly requires removal of the """"""""-1"""""""" nucleosome located on the upstream side of the promoter. The genomic location of ~200 gene- and chromatin-regulatory proteins have been determined at low resolution by ChIP-chip, under normal and heat shock conditions. The data is now being analyzed. High resolution mapping will be achieved by retrofitting the ChIP-chip libraries for ChIP-seq. Even higher resolution mapping will be achieved on a select set of factors using reagents to trim the ChIP DNA. Relationships among binding events will provide new insights into transcription complex assembly and regulation.
Our cells are constantly faced with environmental extremes, involving temperature, starvation, radiation and harmful chemicals. How we deal with this stress depends upon the action of our transcription machinery on genes. Therefore a broad understanding of how our transcription machinery works in the face of various stresses is essential for a physiological understanding of human health.
| Vinayachandran, Vinesh; Reja, Rohit; Rossi, Matthew J et al. (2018) Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock. Genome Res : |
| Yamada, Naomi; Lai, William K M; Farrell, Nina et al. (2018) Characterizing protein-DNA binding event subtypes in ChIP-exo data. Bioinformatics : |
| Rossi, Matthew J; Lai, William K M; Pugh, B Franklin (2018) Simplified ChIP-exo assays. Nat Commun 9:2842 |
| Niu, Ben; Coslo, Denise M; Bataille, Alain R et al. (2018) In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets. Nucleic Acids Res 46:8385-8403 |
| Rossi, Matthew J; Lai, William K M; Pugh, B Franklin (2018) Genome-wide determinants of sequence-specific DNA binding of general regulatory factors. Genome Res 28:497-508 |
| Miller, Jason E; Zhang, Liye; Jiang, Haoyang et al. (2018) Genome-Wide Mapping of Decay Factor-mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4. G3 (Bethesda) 8:315-330 |
| Mahony, Shaun; Pugh, B Franklin (2015) Protein-DNA binding in high-resolution. Crit Rev Biochem Mol Biol 50:269-83 |
| Chang, Gue Su; Chen, Xiangyun Amy; Park, Bongsoo et al. (2014) A comprehensive and high-resolution genome-wide response of p53 to stress. Cell Rep 8:514-27 |
| Nakahashi, Hirotaka; Kieffer Kwon, Kyong-Rim; Resch, Wolfgang et al. (2013) A genome-wide map of CTCF multivalency redefines the CTCF code. Cell Rep 3:1678-1689 |
| Li, Jian; Liu, Yingyun; Rhee, Ho Sung et al. (2013) Kinetic competition between elongation rate and binding of NELF controls promoter-proximal pausing. Mol Cell 50:711-22 |
Showing the most recent 10 out of 17 publications
