Chromatin landscape dictates HSF binding to target DNA elements

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 sequencebinding 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. © 2010 guertin,lis.