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Tiling ChIP-CHIP Ssn6-GFP, Tp11-GFP, Tup12-GFP; Hst4 vs WT Expression

ABSTRACT: Tiling ChIP-CHIP Ssn6-GFP, Tp11-GFP, Tup12-GFP and Hst4 vs WT Expression

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE36429 | GEO | 2012/03/13

SECONDARY ACCESSION(S): PRJNA153235

REPOSITORIES: GEO

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Tiling ChIP-CHIP Ssn6-GFP, Tp11-GFP, Tup12-GFP; Hst4 vs WT Expression

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Project description:The yeast Ssn6-Tup1 complex regulates gene expression through a variety of mechanisms, including positioning of nucleosomes over promoters of some target genes to limit accessibility to the transcription machinery. To further define the functions of Ssn6-Tup1 in gene regulation and chromatin remodeling, we performed genome-wide profiling of changes in nucleosome organization and gene expression that occur upon loss of SSN6 or TUP1, and observed extensive nucleosome alterations in both promoters and gene bodies of derepressed genes. Our improved nucleosome profiling and analysis approaches revealed low-occupancy promoter nucleosomes (P nucleosomes) at locations previously defined as nucleosome-free regions. In the absence of SSN6 or TUP1, this P nucleosome is frequently lost, whereas nucleosomes are gained at -1 and +1 positions, accompanying up-regulation of downstream genes. Our analysis of public ChIP-seq data revealed that Ssn6 and Tup1 preferentially bind TATA-containing promoters, which are also enriched in genes derepressed upon loss of SSN6 or TUP1. These results suggest that stabilization of the P nucleosome on TATA-containing promoters may be a central feature of the repressive chromatin architecture created by the Ssn6-Tup1 corepressor, and that releasing the P nucleosome contributes to gene activation.

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