转录因子(TFs)与称为转录因子结合位点(TFBS)的DNA特定区域结合,并通过与转录机制相互作用来调节基因表达。TFBS通常位于靶基因的上游,在转录起始位点的几千个碱基对内。TFs与TFBS的结合会影响转录机制的募集,从而以精确和特异的方式调节基因转录。本章提供了实际的例子和案例研究,证明了从基因组中提取上游基因区域,使用PWMEnrichR/Bioconductor封装识别TFBS,对结果的解释,并编制可供出版的数字和表格。EOMES启动子用作单个DNA序列分析的案例研究,揭示了LHX9-FOXP1复合物在胚胎发育过程中的潜在调控。此外,一个例子是关于如何研究一组基因的上游区域的TFBS,使用对人类副流感病毒1型(HPIV1)感染和干扰素-β的差异表达基因的案例研究。在这种情况下确定的关键调节因子包括STAT1:STAT2异二聚体和干扰素调节因子家族蛋白。所提出的协议旨在使具有基本计算机知识的个人可以访问。了解TFs和TFBS之间的相互作用提供了对控制基因表达的复杂转录调控网络的见解。对发育生物学等几个领域有着广泛的影响,免疫学,和疾病研究。
Transcription factors (TFs) bind to specific regions of DNA known as transcription factor binding sites (TFBSs) and modulate gene expression by interacting with the transcriptional machinery. TFBSs are typically located upstream of target genes, within a few thousand base pairs of the transcription start site. The binding of TFs to TFBSs influences the recruitment of the transcriptional machinery, thereby regulating gene transcription in a precise and specific manner. This chapter provides practical examples and
case studies demonstrating the extraction of upstream gene regions from the genome, identification of TFBSs using PWMEnrich R/Bioconductor package, interpretation of results, and preparation of publication-ready figures and tables. The EOMES promoter is used as a
case study for single DNA sequence analysis, revealing potential regulation by the LHX9-FOXP1 complex during embryonic development. Additionally, an example is presented on how to investigate TFBSs in the upstream regions of a group of genes, using a
case study of differentially expressed genes in response to human parainfluenza virus type 1 (HPIV1) infection and interferon-beta. Key regulators identified in this context include the STAT1:STAT2 heterodimer and interferon regulatory factor family proteins. The presented protocol is designed to be accessible to individuals with basic computer literacy. Understanding the interactions between TFs and TFBSs provides insights into the complex transcriptional regulatory networks that govern gene expression, with broad implications for several fields such as developmental biology, immunology, and disease research.