ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes (PRO-seq)

Transcription factors bind to sequence motifs and act as activators or repressors. Transcription factors interface with a constellation of accessory cofactors to regulate distinct mechanistic steps to regulate transcription. We rapidly degraded the essential and ubiquitously expressed transcription factor ZNF143 to determine its function in the transcription cycle. ZNF143 facilitates RNA Polymerase initiation and activates gene expression. ZNF143 binds the promoter of nearly all its activated target genes. Paradoxically, ZNF143 binds near the site of genic transcription initiation to directly repress a subset of genes. Although ZNF143 stimulates initiation at ZNF143-repressed genes (i.e. those that increase expression upon ZNF143 depletion), the molecular context of binding leads to cis repression. ZNF143 competes with other more efficient activators for promoter access, physically occludes transcription initiation sites, and acts as a molecular roadblock to RNA Polymerase to repress genes in cis. The term "context specific" is often invoked to describe transcription factors that have both activation and repression functions. Here, we define the context and molecular mechanisms of ZNF143-mediated cis activation and repression. HEK293T cells with ZNF143 tagged with an inducible degron tag were treated with drugs to induce ZNF143 degradation for 30 minutes, then collected for PRO-seq.

转录因子（Transcription factor）可结合序列基序，并作为激活因子或阻遏因子发挥功能。转录因子可与一系列辅助辅因子相互作用，调控转录过程中的不同机制步骤。本研究通过快速降解在细胞中广泛表达的必需转录因子ZNF143，以解析其在转录循环中的功能。ZNF143可促进RNA聚合酶（RNA Polymerase）的起始过程，并激活基因表达。ZNF143可结合其几乎所有激活型靶基因的启动子区域。矛盾的是，ZNF143还可结合基因转录起始位点附近区域，直接抑制部分基因的表达。尽管ZNF143可在其阻遏的靶基因（即ZNF143降解后表达量上调的基因）上促进转录起始，但结合的分子环境会介导顺式阻遏效应。ZNF143可与其他更高效的激活因子竞争启动子结合位点，物理遮蔽转录起始位点，并作为RNA聚合酶的分子路障，从而顺式抑制基因表达。"环境特异性"这一术语常被用于描述兼具激活与阻遏功能的转录因子。本研究明确了ZNF143介导的顺式激活与阻遏的作用环境及分子机制。将带有诱导型降解标签（inducible degron tag）的ZNF143的HEK293T细胞用药物处理30分钟以诱导ZNF143降解，随后收集细胞进行PRO-seq测序。