Genomics

Dataset Information

24

Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription [Affymetrix]


ABSTRACT: The Saccharomyces cerevisiae protein Nhp6A is a model for the abundant and multifunctional HMGB family of chromatin-associated proteins. Nhp6A binds DNA in vitro without sequence-specificity and bends DNA sharply, but its role in chromosome biology is poorly understood. We show by whole genome ChIP-chip that Nhp6A is localized to specific regions of chromosomes that include about 23% of RNA polymerase II promoters. Nhp6A binding functions to stabilize positioned nucleosomes within promoter and 5' coding regions of these genes. Both genomic binding and transcript expression studies point to functionally-related groups of genes that are specifically bound by Nhp6A and whose transcription is altered by the absence of Nhp6. Genomic analyses of Nhp6A mutants specifically defective in DNA bending reveals a critical role of DNA bending for co-regulation of transcription but not for targeted binding by Nhp6A. Overall design: Nhp6A (WT and point mutants) were ChIPed using a polyclonal antibody. Histone H3 was ChIPed using a commercially available antibody. IP experiments were compared to two sonicated, crosslinked chromatin samples (Input).

INSTRUMENT(S): [Sc03b_MR] Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array

SUBMITTER: Noah L. Dowell  

PROVIDER: GSE23582 | GEO | 2010-09-15

SECONDARY ACCESSION(S): PRJNA133373

REPOSITORIES: GEO

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Publications

Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription.

Dowell Noah L NL   Sperling Adam S AS   Mason Michael J MJ   Johnson Reid C RC  

Genes & development 20100901 18


The Saccharomyces cerevisiae protein Nhp6A is a model for the abundant and multifunctional high-mobility group B (HMGB) family of chromatin-associated proteins. Nhp6A binds DNA in vitro without sequence specificity and bends DNA sharply, but its role in chromosome biology is poorly understood. We show by whole-genome chromatin immunoprecipitation (ChIP) and high-resolution whole-genome tiling arrays (ChIP-chip) that Nhp6A is localized to specific regions of chromosomes that include ∼23% of RNA p  ...[more]

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