Chromatin Landscape Dictates HSF Binding to Target DNA Elements

Abstract

Sequence-specific transcription factors (TFs) are critical for specifying patterns and levels of gene expression, but target DNA elements are not sufficient to specify TF binding in vivo. In eukaryotes, the binding of a TF is in competition with a constellation of other proteins, including histones, which package DNA into nucleosomes. We used the ChIP-seq assay to examine the genome-wide distribution of Drosophila Heat Shock Factor (HSF), a TF whose binding activity is mediated by heat shock-induced trimerization. HSF binds to 464 sites after heat shock, the vast majority of which contain HSF Sequence-binding Elements (HSEs). HSF-bound sequence motifs represent only a small fraction of the total HSEs present in the genome. ModENCODE ChIP-chip datasets, generated during non-heat shock conditions, were used to show that inducibly bound HSE motifs are associated with histone acetylation, H3K4 trimethylation, RNA Polymerase II, and coactivators, compared to HSE motifs that remain HSF-free. Furthermore, directly changing the chromatin landscape, from an inactive to an active state, permits inducible HSF binding. There is a strong correlation of bound HSEs to active chromatin marks present prior to induced HSF binding, indicating that an HSE's residence in “active” chromatin is a primary determinant of whether HSF can bind following heat shock.

Author Summary

Many Transcription Factors (TFs) have been shown to bind DNA in a sequence-specific manner. However, only a sub-set of possible binding sites are occupied in vivo, and it remains unclear how TFs discriminate between sequences of equal predicted binding affinity. We set out to determine how a specific TF, Heat Shock Factor (HSF), distinguishes between utilized and unused potential binding sites. HSF is uniquely qualified to study this problem, because HSF is inactive and lowly bound to DNA in unstressed cells and upon stress HSF becomes active and strongly binds to DNA. We compared the properties of the unstressed chromatin between the sites that become HSF-bound or remain HSF-free following stress activation. We find that sites that are destined to be bound strongly by HSF after stress are associated with distinct chromatin marks compared to sites that are unoccupied by HSF after heat shock. Furthermore, chromatin landscape can be changed from a restrictive to a permissive state, allowing inducible HSF binding. These finding suggest that TF binding sites can be predicted based on the chromatin signatures present prior to induced TF recruitment.