Joint sequence and chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin (ATAC-seq)

The DNA-binding activities of transcription factors (TFs) are influenced by both intrinsic sequence preferences and extrinsic interactions with cell-specific chromatin landscapes and other regulatory proteins. Disentangling the roles of these determinants in TF-DNA binding remains challenging. For instance, the FoxA subfamily of Forkhead domain TFs are known pioneer factors, yet their binding varies across cell types, pointing to a combination of intrinsic and extrinsic forces guiding their binding. How such sequence and chromatin influences vary across related Forkhead domain TFs remains mostly uncharacterized. Here, we present a principled approach to compare the relative contributions of intrinsic DNA sequence preference and cell-specific chromatin environments to a TF’s DNA-binding activities. We over-express a selection of Fox TFs in mouse embryonic stem (mES) cells, which offer a platform to contrast each TF's binding activity within the same preexisting chromatin background. By developing and applying a neural network that jointly models sequence and chromatin data, we can evaluate how sequence and preexisting chromatin features contribute to induced TF binding, both at individual sites and genome-wide. We demonstrate that Fox TFs bind different DNA targets, and drive differential gene expression patterns, even when induced in identical chromatin settings. Differential Fox binding activities can be attributed to distinct DNA-binding preferences coupled with differential abilities to engage relatively inaccessible chromatin. We propose that varying preferences for preexisting chromatin states enables the functional diversification of paralogous TFs. Genome-wide ATAC-seq profiling of chromatin accessibility after over-expression of selected Forkhead domain transcription factors in mouse embryonic stem cells

转录因子（transcription factors, TFs）的DNA结合活性同时受到内在序列偏好性，以及与细胞特异性染色质景观、其他调控蛋白的外在相互作用的双重影响。厘清这些决定因素在TF-DNA结合过程中的作用仍颇具挑战。例如，叉头框（Forkhead）结构域转录因子的FoxA亚家族属于公认的先锋因子，但其结合模式却随细胞类型不同而存在差异，提示其结合过程由内在与外在因素共同调控。目前，此类序列与染色质影响在相关叉头框结构域转录因子间的差异特征仍未得到充分解析。本研究提出一套严谨的分析方法，用于对比内在DNA序列偏好性与细胞特异性染色质环境对转录因子DNA结合活性的相对贡献。我们在小鼠胚胎干细胞（mouse embryonic stem cells, mES）中过表达一组Fox转录因子，该细胞系可作为统一平台，在相同的预存染色质背景下对比各转录因子的结合活性。通过开发并应用一种可联合建模序列与染色质数据的神经网络，我们可在单个结合位点与全基因组层面，评估序列与预存染色质特征对诱导型TF结合的贡献程度。研究结果表明，即使在完全一致的染色质环境中诱导表达，不同Fox家族转录因子仍会结合不同的DNA靶标，并驱动差异化的基因表达模式。Fox家族转录因子的差异化结合活性，可归因于其独特的DNA结合偏好性，以及靶向相对染色质不可及区域的差异化能力。我们提出，对预存染色质状态的差异化偏好，可促使旁系同源转录因子实现功能多样化。本数据集包含在小鼠胚胎干细胞中过表达选定叉头框结构域转录因子后，针对染色质可及性开展的全基因组ATAC测序（ATAC-seq）分析数据。