Analysis abstract
Nature Genetics 39, 303 - 309 (2007)
Published online: 26 February 2007 | doi:10.1038/ng1965
A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription
Israel Steinfeld1,2, Ron Shamir2 & Martin Kupiec1
Abstract
Chromatin structure is important in transcription regulation. Many factors influencing chromatin structure have been identified, but the transcriptional programs in which they participate are still poorly understood. Chromatin modifiers participate in transcriptional control together with DNA-bound transcription factors. High-throughput experimental methods allow the genome-wide identification of binding sites for transcription factors as well as quantification of gene expression under various environmental and genetic conditions. We have developed a new methodology that uses the vast amount of available data to dissect the contribution of chromatin structure to transcription. We measure and characterize the dependence of transcription factor function on specific chromatin modifiers. We apply our methodology to S. cerevisiae, using a compendium of 170 gene expression profiles of strains defective for chromatin modifiers, taken from 26 different studies. Our method succeeds in identifying known intricate genetic interactions between chromatin modifiers and transcription factors and uncovers many previously unknown genetic interactions, giving the first genome-wide picture of the contribution of chromatin structure to transcription in a eukaryote.
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
- School of Computer Science, Tel Aviv University, Ramat Aviv 69978, Israel.
Correspondence to: Martin Kupiec1 e-mail: martin@post.tau.ac.il
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