Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1.
Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1.
复制标题
对影响先锋因子结合特异性的序列特征的系统剖析揭示了 FOXA1 和 AP-1 之间的结合协同作用。
DOI：
10.1101/2023.11.08.566246
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Bai,Lu
中科院分区：
文献类型：
--
作者：
Xu,Cheng;Kleinschmidt,Holly;Yang,Jianyu;Leith,Erik;Johnson,Jenna;Tan,Song;Mahony,Shaun;Bai,Lu
尽管先锋因子(PFS)在封闭的染色质中具有靶向核小体位置的独特能力，但它们只结合了一小部分基因组基序。这种选择性的潜在机制还不是很清楚。在这里，我们设计了一种名为染色质免疫沉淀与整合合成寡核苷酸(CHIP-ISO)的高通量分析，以系统地分析影响经典PF FOXA1在人A549细胞中结合特异性的序列特征。结合CHIP-ISO在体外和神经网络的分析，我们发现(1)FOXA1结合强烈地受到共结合转录因子AP-1和CEBPB的影响；(2)FOXA1和AP-1在体外表现出结合的协同作用；(3)FOXA1‘S结合更多地由局部序列决定，而不是染色质环境，包括EU-/异染色质；(4)AP-1在不同细胞类型中部分负责FOXA1的差异结合。我们的研究提出了一个框架，用于阐明潜在的PF结合特异性的遗传规则，并揭示了对其结合的上下文特定调节机制。
Despite the unique ability of pioneer factors (PFs) to target nucleosomal sites in closed chromatin, they only bind a small fraction of their genomic motifs. The underlying mechanism of this selectivity is not well understood. Here, we design a high-throughput assay called chromatin immunoprecipitation with integrated synthetic oligonucleotides (ChIP-ISO) to systematically dissect sequence features affecting the binding specificity of a classic PF, FOXA1, in human A549 cells. Combining ChIP-ISO within vitroand neural network analyses, we find that (1) FOXA1 binding is strongly affected by co-binding transcription factors (TFs) AP-1 and CEBPB; (2) FOXA1 and AP-1 show binding cooperativityin vitro; (3) FOXA1's binding is determined more by local sequences than chromatin context, including eu-/heterochromatin; and (4) AP-1 is partially responsible for differential binding of FOXA1 in different cell types. Our study presents a framework for elucidating genetic rules underlying PF binding specificity and reveals a mechanism for context-specific regulation of its binding.