Activation domains and Coactivator direct genomic localization of fused DNA binding domains, defining the subset of activated promoters [RNA-seq]

Activation domains (ADs) within transcription factors (TFs) induce gene expression by recruiting coactivators to specific regulatory regions. Within the prevailing model, TF-coactivator recruitment is independent of DNA binding, which is consistent with direct AD-coactivator interactions seen outside cells. However, this independence was not yet tested within the genomic context. Here, we targeted two Med15-interacting ADs to hundreds of budding yeast promoters through fusions with multiple DNA binding domains (DBDs), gradually controlling their abundances using libraries of synthetic promoters. Genomic profiling revealed that AD identity influences DNA binding locations and that transcription induction and Med15 recruitment are restricted to a subset of DBD-bound promoters displaying flexible expression, multiple-TFs binding, and fuzzy nucleosome architecture. Further, when fused to a DBD, Med15 redirected binding towards promoters of fuzzy nucleosomes, overcoming DBD-based preferences. Our results demonstrate that ADs and their recruited coactivators posses an inherent preference for genomic localization and, therefore, define the subset of induced promoters.转录因子（transcription factors, TFs）内的激活结构域（activation domains, ADs）可通过将共激活因子招募至特定调控区域来诱导基因表达。当前主流模型认为，转录因子与共激活因子的招募过程不依赖DNA结合，这与细胞外观测到的激活结构域-共激活因子直接相互作用结果相符。然而，这一独立性尚未在基因组环境中得到验证。本研究通过将两个与Med15相互作用的激活结构域与多种DNA结合结构域（DNA binding domains, DBDs）融合，将其靶向至数百个出芽酵母启动子区域，并借助合成启动子文库逐步调控其表达丰度。基因组谱分析显示，激活结构域的特性会影响DNA结合位点的选择；转录诱导与Med15招募仅局限于一类结合了DNA结合结构域的启动子子集，这类启动子具备动态表达、多转录因子结合以及模糊核小体结构的特征。进一步研究发现，当与DNA结合结构域融合后，Med15可将结合重定向至模糊核小体富集的启动子区域，突破了DNA结合结构域自身的结合偏好。本研究结果证实，激活结构域及其招募的共激活因子对基因组定位具有固有偏好，进而界定了被诱导激活的启动子子集。