Systematic investigation of transcription factor activity in the context of chromatin using massively parallel DNA binding and expression assays
Ontology highlight
ABSTRACT: Precise gene expression patterns are established by timely and specific binding of transcription factors (TFs) to regulatory sequences. While these events occur in the context of chromatin, our understanding of how TF-nucleosome interplay affects gene expression is highly limited. Here we present a novel assay for high-resolution measurements of both DNA occupancy and gene expression on large-scale libraries of systematically designed regulatory sequences. Our assay is capable of revealing occupancy patterns at the single–cell level. It provides an accurate quantification of the fraction of the population bound by a nucleosome and captures distinct, even adjacent, TF binding events. By applying this assay to over 1500 promoter variants in yeast, we reveal pronounced differences in the dependency of TF activity on chromatin. Our approach provides means to classify TFs by their differential capacity to alter chromatin and promote expression. We further demonstrate how different regulatory sequences give rise to nucleosome-mediated TF collaborations that quantitatively account for the resulting expression. We show the utility of this approach in dissecting the logic of native regulatory sequences, highlighting the importance of TF-nucleosome interactions in the quantitative readout of regulatory information
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE92300 | GEO | 2017/02/16
SECONDARY ACCESSION(S): PRJNA357133
REPOSITORIES: GEO
ACCESS DATA