Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.
PLoS Genet. 2010 Sep 9;6(9):e1001114. doi: 10.1371/journal.pgen.1001114.
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.
序列特异性转录因子（TFs）对于指定基因表达的模式和水平至关重要，但靶 DNA 元件不足以在体内指定 TF 结合。在真核生物中，TF 的结合与一系列其他蛋白质（包括组蛋白）竞争，组蛋白将 DNA 包装成核小体。我们使用 ChIP-seq 测定法来研究果蝇热休克因子（HSF）的全基因组分布，HSF 是一种通过热休克诱导的三聚化介导其结合活性的 TF。HSF 在热休克后结合到 464 个位点，其中绝大多数包含 HSF 序列结合元件（HSEs）。HSF 结合的序列基序仅代表基因组中存在的总 HSE 的一小部分。ModENCODE ChIP-chip 数据集，在非热休克条件下生成，用于显示与 HSF 自由的 HSE 基序相比，可诱导结合的 HSE 基序与组蛋白乙酰化、H3K4 三甲基化、RNA 聚合酶 II 和共激活因子相关。此外，直接改变染色质景观，从非活性状态变为活性状态，允许诱导性 HSF 结合。在诱导性 HSF 结合之前存在的活性染色质标记与结合的 HSE 之间存在很强的相关性，这表明 HSE 在“活性”染色质中的存在是 HSF 在热休克后能否结合的主要决定因素。
