Chromatin opening by p53 is confined by Trim24 in a histone methylation-dependent manner [RNA-seq]

Chromatin modifications are thought to provide additional context dependence for sequence-based gene activation. Binding sites of the transcription factor (TF) and important tumor suppressor p53 are unusually diverse with regards to their chromatin accessibility and histone modifications, suggesting different modes of binding. Here, we show that the ability of p53 to open chromatin and activate its target genes upon DNA damage is locally restricted by its cofactor Trim24. The histone-binding domains of Trim24 limit the role of p53 at closed chromatin but not at accessible chromatin where Trim24 is blocked by histone 3 methylation at lysine 4. In turn p53 regulates gene expression as a function of the naïve chromatin state prior to activation. These findings establish a set of p53 response genes in closed chromatin that are Trim24-regulated and illustrate how histone modification sensing cofactors bridge local chromatin state and TF potency. Examination of p53 and Trim24 function in cell lines including mouse embryonic stem cells. Includes RNAseq in WT mouse ESCs in untreated/p53activated conditions (duplicates), RNAseq in Trim24-degron tagged mouse ESC lines under Trim24degraded/untreated conditions (triplicates), RNAseq in Trim24-degron tagged mouse ESC lines under p53activated/p53activated;Trim24degraded conditions at multiple timepoints of 2/4/8/12 hours (triplicates). All conditions to activate p53 or degrade degron tagged alleles performed for 4 hours unless specified in a timecourse series.

染色质修饰被认为可为基于序列的基因激活过程提供额外的情境依赖性。转录因子（Transcription Factor, TF）与重要肿瘤抑制因子p53的结合位点，在染色质可及性与组蛋白修饰方面呈现出异常多样的特征，提示二者存在不同的结合模式。本研究证实，DNA损伤条件下p53开放染色质并激活靶基因的能力，会被其辅因子Trim24进行局部限制。Trim24的组蛋白结合结构域会限制p53在闭合染色质上的调控功能，但不会影响其在可及染色质中的作用——在可及染色质中，Trim24会被组蛋白H3赖氨酸4位点的甲基化所阻断。反之，p53会依据激活前的初始染色质状态来调控基因表达。本研究结果确立了一组受Trim24调控的闭合染色质p53应答基因，并阐明了组蛋白修饰感知型辅因子如何衔接局部染色质状态与转录因子的调控效能。本研究在包括小鼠胚胎干细胞（ESC）在内的多种细胞系中检测了p53与Trim24的功能。本数据集包含以下RNA测序（RNAseq）样本：野生型（Wild Type, WT）小鼠胚胎干细胞在未处理/p53激活条件下的样本（生物学重复两次）；携带Trim24降解标签的小鼠胚胎干细胞系在Trim24降解/未处理条件下的样本（生物学重复三次）；以及携带Trim24降解标签的小鼠胚胎干细胞系在p53激活 / p53激活且Trim24降解条件下，于2、4、8、12小时多个时间点的样本（生物学重复三次）。除时间进程系列实验外，所有用于激活p53或降解携带降解标签的等位基因的实验均持续4小时。