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.
Highlights
Signal-dependent activation of transcription is a highly regulated process that is dictated by transcriptional activators that selectively identify and function at sequence-specific DNA motifs
Only a subset of possible binding sites are occupied in vivo, and it remains unclear how transcription factors (TFs) discriminate between sequences of equal predicted binding affinity
We find that sites that are destined to be bound strongly by Heat Shock Factor (HSF) after stress are associated with distinct chromatin marks compared to sites that are unoccupied by HSF after heat shock
Summary
Signal-dependent activation of transcription is a highly regulated process that is dictated by transcriptional activators that selectively identify and function at sequence-specific DNA motifs. Two main mechanisms have been proposed that explain the observed in vivo binding specificity (reviewed in [5]): TFs are occluded from cognate site by chromatin structure or TF binding is facilitated by cooperative interactions with cofactors. Sequencespecific ChIP experiments of homeoproteins revealed that binding sites are preferentially accessible if target motifs are located within active genes [1]. The Hox proteins primarily discriminate between equivalent predicted binding sites by cooperative interactions with DNA-bound cofactors (reviewed in [11]). These findings indicate that the binding of TFs depend upon the chromatin landscape as well as specific sequence elements, and we set out to determine the extent to which chromatin affects TF binding genome-wide. Characterizing the mechanistic parameters by which TFs locate and bind to target DNA sequences will provide insight into a critical early step in a cell’s ability to orchestrate patterns of gene expression in response to developmental, nutritional, and environmental signals
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