ChIP-seq of Abf1, TATA-binding protein, and RNA Polymerase II in wild type and abf1 temperature sensitive mutant yeast (Saccharomyces cerevisiae)
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Saccharomyces cerevisiae S288c
SUBMITTER: Randall Morse
PROVIDER: E-MTAB-3208 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:ChIP-seq of Abf1, TATA-binding protein, and RNA Polymerase II in wild type and abf1 temperature sensitive mutant yeast (Saccharomyces cerevisiae)
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Project description:We grew wild type and corresponding mutant abf1 and rap1 temperature sensitive yeast at 25 C, then for one hour after shifting to 37 C. We then prepared nucleosomal (mostly mononucleosomal) DNA and hybridized to tiling arrays. Three abf1 ts mutant and corresponding wild type, and three rap1 ts mutant and corresponding wild type (note not the same wild type; BY4741 for Rap1, but TMY86 for Abf1)
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Project description:Abf1 has been defined as a general regulatory factor involved in determining chromatin structure in the yeast Saccharomyces cerevisiae. As such, it plays a major role in a range of functions including DNA replication, transcriptional activation and gene silencing, as well as DNA repair. Previous studies have identified an Abf1 DNA consensus binding sequence and Abf1 binding at up to several hundred locations throughout the genome. Depletion of Abf1 in the cell, however, results in altered nucleosome structure at many thousands of sites throughout the yeast genome, suggesting a far greater role for Abf1 in chromatin structure and dynamics. Here, we examine genome-wide Abf1 binding using ChIP-Chip to measure its chromatin occupancy. Using a novel software package, Sandcastle, we detect 3,821 genomic positions at which Abf1 binds. We conducted a detailed bioinformatic analysis of these novel Abf1 binding sites, defining variations in the current consensus sequence and identifying many more genomic locations at which Abf1 can be found. These observations define the sites at which Abf1 occupancy determines chromatin structure, providing a framework for understanding how processes such as replication, transcription and DNA repair are organised within the genome.
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