Accurate prediction of inducible transcription factor binding intensities in vivo.
Accurate prediction of inducible transcription factor binding intensities in vivo.
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DOI：
10.1371/journal.pgen.1002610
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Lis JT
中科院分区：
文献类型：
--
作者：
Guertin MJ;Martins AL;Siepel A;Lis JT
DNA序列和局部染色质景观共同作用，以确定转录因子（TF）的结合强度分布。为了解开这些影响，我们开发了一种实验方法，称为蛋白质/DNA结合，然后进行高通量测序（PB-seq），该方法允许在没有染色质的情况下在全基因组范围内表征结合能景观。我们将我们的方法应用于果蝇热休克因子（HSF），其在热休克应激后诱导结合靶DNA序列元件（HSE）。PB-seq涉及将剪切的裸基因组DNA与重组HSF一起孵育，分配HSF结合的DNA和HSF游离的DNA，然后通过高通量测序检测HSF结合的DNA。我们将PB-seq结合谱与ChIP-seq在体内观察到的结合谱进行了比较，并开发了统计模型，以基于描述局部染色质环境的协变量预测观察到的与理想结合模式的偏离。我们发现，DNase I超敏反应和H4的四乙酰化是预测HSF结合亲和力变化的最有影响力的协变量。我们还研究了通过数字DNase I足迹数据测量的DNA可及性，可以从MNase-seq数据和ChIP芯片图谱中预测许多组蛋白修饰和TF的程度，并发现GAGA元件相关因子（GAF），H4的四乙酰化和H4 K16乙酰化是最具预测性的协变量。最后，我们产生了一个公正的模型HSF结合序列，揭示了不同的生物物理特性的HSF/HSE相互作用和以前未被识别的子结构内的HSE。这些发现为基因组序列和染色质景观在确定转录因子结合强度方面的相互作用提供了新的见解。转录因子（TF）结合DNA以调节基因表达水平。TF结合位点在整个发育过程中变化，以响应环境刺激，不同的组织具有不同的TF结合特征。TF以上下文依赖的方式区分结合位点的机制是一个活跃的研究领域，但很明显，潜在结合位点所在的染色质环境强烈影响结合。本研究使用热休克TF（HSF）研究染色质对诱导HSF结合的影响。我们实施了一项实验技术，以量化基因组中所有潜在的HSF结合位点。在HSF结合之前，将这些数据与染色质景观信息一起沿着纳入建模框架中，以准确预测诱导型HSF结合位点的强度。DNA酶I超敏反应和H4的四乙酰化是模型中最具影响力的协变量。结合数据使一个更完整的HSF/DNA相互作用模型的发展，提供洞察HSF三聚体亚基和靶DNA五聚体的生物物理相互作用。
DNA sequence and local chromatin landscape act jointly to determine transcription factor (TF) binding intensity profiles. To disentangle these influences, we developed an experimental approach, called protein/DNA binding followed by high-throughput sequencing (PB–seq), that allows the binding energy landscape to be characterized genome-wide in the absence of chromatin. We applied our methods to the Drosophila Heat Shock Factor (HSF), which inducibly binds a target DNA sequence element (HSE) following heat shock stress. PB–seq involves incubating sheared naked genomic DNA with recombinant HSF, partitioning the HSF–bound and HSF–free DNA, and then detecting HSF–bound DNA by high-throughput sequencing. We compared PB–seq binding profiles with ones observed in vivo by ChIP–seq and developed statistical models to predict the observed departures from idealized binding patterns based on covariates describing the local chromatin environment. We found that DNase I hypersensitivity and tetra-acetylation of H4 were the most influential covariates in predicting changes in HSF binding affinity. We also investigated the extent to which DNA accessibility, as measured by digital DNase I footprinting data, could be predicted from MNase–seq data and the ChIP–chip profiles for many histone modifications and TFs, and found GAGA element associated factor (GAF), tetra-acetylation of H4, and H4K16 acetylation to be the most predictive covariates. Lastly, we generated an unbiased model of HSF binding sequences, which revealed distinct biophysical properties of the HSF/HSE interaction and a previously unrecognized substructure within the HSE. These findings provide new insights into the interplay between the genomic sequence and the chromatin landscape in determining transcription factor binding intensity. Transcription factors (TFs) bind DNA to modulate levels of gene expression. TF binding sites change throughout development, in response to environmental stimuli, and different tissues have distinct TF binding profiles. The mechanism by which TFs discriminate between binding sites in a context dependent manner is an area of active research, but it is clear that the chromatin environment in which potential binding sites reside strongly influences binding. This study used the Heat Shock TF (HSF) to study the effect chromatin has upon induced HSF binding. We implemented an experimental technique to quantify all potential HSF binding sites in the genome. These data were incorporated into a modeling framework along with chromatin landscape information prior to HSF binding to accurately predict the intensities of inducible HSF binding sites. DNase I hypersensitivity and tetra-acetylation of H4 were the most influential covariates in the model. The binding data enabled the development of a more complete HSF/DNA interaction model, providing insight into the biophysical interaction of HSF trimer subunits and target DNA pentamers.
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