The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation
The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation
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DOI：
10.1093/g3journal/jkad269
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发表时间：
2023-11-22
影响因子：
2.6
通讯作者：
Bhattacharyya，Tapas
中科院分区：
文献类型：
--
作者：
Long，Trevor;Bhattacharyya，Tapas
在基因调控过程中，DNA的可接近性被认为限制了转录因子（TF）结合位点的可用性，而TF可以增加DNA的可接近性，以招募其他上调基因表达的因子。鉴于这种相互作用，对绝大多数基因来说，基因表达调节中的致病调节事件仍然未知。我们利用深度测序的ATAC-Seq数据和位点特异性敲入报告基因来研究DNA可及性的结合位点解析动态与巨噬细胞-中性粒细胞分化过程中增强子表达动态之间的关系。虽然增强子在分化的早期阶段上调了报告基因的表达，但它们的总可及性却没有相应的增加。相反，总可达性在分化的最后阶段达到峰值，但增强子活性没有增加。在分化早期，C/ ebp家族TF结合位点附近的可达性显著增加，表明TF占用，表明增强子活性的早期上调是由TF结合驱动的。这些结果表明，DNA可及性的普遍增加是不够的，增强子特异性tf的结合是基因表达上调的必要条件。此外，高覆盖率的ATAC-Seq结合时间序列表达数据可以在结合位点分辨率上推断出调控事件的顺序。
During gene regulation, DNA accessibility is thought to limit the availability of transcription factor (TF) binding sites, while TFs can increase DNA accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events in the modulation of gene expression remain unknown for the vast majority of genes. We utilized deeply sequenced ATAC-Seq data and site-specific knock-in reporter genes to investigate the relationship between the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers ofCebpaduring macrophage-neutrophil differentiation. While the enhancers upregulate reporter expression during the earliest stages of differentiation, there is little corresponding increase in their total accessibility. Conversely, total accessibility peaks during the last stages of differentiation without any increase in enhancer activity. The accessibility of positions neighboring C/EBP-family TF binding sites, which indicates TF occupancy, does increase significantly during early differentiation, showing that the early upregulation of enhancer activity is driven by TF binding. These results imply that a generalized increase in DNA accessibility is not sufficient, and binding by enhancer-specific TFs is necessary, for the upregulation of gene expression. Additionally, high-coverage ATAC-Seq combined with time-series expression data can infer the sequence of regulatory events at binding-site resolution.