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Activation domains and Coactivator direct genomic localization of fused DNA binding domains, defining the subset of activated promoters [RNA-seq]

ABSTRACT: Activation domains (ADs) within transcription factors (TFs) induce gene expression by recruiting coactivators to specific regulatory regions. Within the prevailing model, TF-coactivator recruitment is independent of DNA binding, which is consistent with direct AD-coactivator interactions seen outside cells. However, this independence was not yet tested within the genomic context. Here, we targeted two Med15-interacting ADs to hundreds of budding yeast promoters through fusions with multiple DNA binding domains (DBDs), gradually controlling their abundances using libraries of synthetic promoters. Genomic profiling revealed that AD identity influences DNA binding locations and that transcription induction and Med15 recruitment are restricted to a subset of DBD-bound promoters displaying flexible expression, multiple-TFs binding, and fuzzy nucleosome architecture. Further, when fused to a DBD, Med15 redirected binding towards promoters of fuzzy nucleosomes, overcoming DBD-based preferences. Our results demonstrate that ADs and their recruited coactivators posses an inherent preference for genomic localization and, therefore, define the subset of induced promoters.

ORGANISM(S): Saccharomyces cerevisiae BY4741

PROVIDER: GSE234431 | GEO | 2023/12/19

REPOSITORIES: GEO

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Transcription factors activate genes through the phase separation capacity of their activation domains [RNA-seq]

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2018-10-26 | GSE120474 | GEO

Transcription factors activate genes through the phase separation capacity of their activation domains [ChIP-seq]

2018-10-26 | GSE120459 | GEO

A Med15 - Hrp1 complex associates with fission yeast Mediator

Project description:The multiprotein Mediator complex is an important regulator of RNA polymerase II-dependent genes in eukaryotic cell. In contrast to the situation in many other eukaryotes, the conserved Med15 protein is not a stable component of Mediator isolated from fission yeast. We now demonstrate that Med15 exists in a protein complex together with Hrp1, an ATP-dependent chromatin remodeling protein. The Med15/Hrp1 subcomplex is not a component of the core Mediator complex, but can interact with the repressive L-Mediator conformation. Deletion of MED15 and HRP1 cause similar effects on global steady-state levels of mRNA, but only MED15 is required for galactose-dependent activation of the inv1 gene. Hrp1 has been found in complex with other proteins and genome-wide analysis demonstrates that Med15 only associates with a distinct subset of Hrp1-bound gene promoters. Global analysis reveals that Hrp1-binding normally is associated with increased histone H3 density, but at promoters also bound by Med15, histone H3 density is instead increased. Our findings reveal that Med15 functions as a separate entity in fission yeast and indicate that the function and organization of the Mediator complex may differ significantly between eukaryotes. Keywords: ChIP-chip

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Knockout of the DNA binding domains in human-specific lncRNAs causes changed expression of target genes

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ChIP-seq of Mediator subunits in Mediator mutants and wild type yeast

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Corepressors (NCoR and SMRT) as well as Coactivators are Recruited to Positively Regulated 1α,25-Dihydroxyvitamin D3-Responsive Genes

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2012-09-05 | E-GEOD-39277 | biostudies-arrayexpress

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2013-06-07 | E-GEOD-47712 | biostudies-arrayexpress

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