Chromatin regulation of transcriptional enhancers and cell fate by the Sotos syndrome gene NSD1 [TT-Seq]

Nuclear-receptor-binding SET-domain protein 1 (NSD1), a methyltransferase that catalyzes H3K36me2, is essential for mammalian development and frequently dysregulated in diseases, including Sotos syndrome. Despite impacts of H3K36me2 on H3K27me3 and DNA methylation, a direct role of NSD1 in transcriptional regulation remains largely unknown. Here, we show that NSD1 and H3K36me2 are enriched at cis-regulatory elements, particularly enhancers. NSD1 enhancer association is conferred by a tandem quadruple PHD-PWWP module, which recognizes p300-catalyzed H3K18ac. By combining acute NSD1 depletion with time-resolved epigenomic and nascent transcriptomic analyses, we demonstrate that NSD1 promotes enhancer-dependent gene transcription by facilitating RNA polymerase II pause release. Notably, NSD1 can act as a transcriptional coactivator independent of its catalytic activity. Moreover, NSD1 enables activation of developmental transcriptional programs associated with Sotos syndrome pathophysiology and controls ESC multilineage differentiation. Collectively, we have identified NSD1 as an enhancer-acting transcriptional coactivator that contributes to cell fate transition and Sotos syndrome development. TT-seq was performed with NSD1-dTAG mESCs after 0, 1, and 6h of dTAG-13 treatment.

核受体结合SET结构域蛋白1（NSD1）是一类催化H3K36me2的甲基转移酶，对哺乳动物发育至关重要，且在包括索托斯综合征在内的多种疾病中常发生失调。尽管H3K36me2对H3K27me3与DNA甲基化具有调控作用，但NSD1在转录调控中的直接功能仍未得到充分解析。本研究发现，NSD1与H3K36me2富集于顺式调控元件，尤其是增强子区域。NSD1与增强子的结合由串联四重PHD-PWWP结构域模块介导，该模块可识别p300催化生成的H3K18ac。本研究通过将急性NSD1降解与时间分辨表观基因组学、新生转录组学分析相结合，证实NSD1可通过促进RNA聚合酶II的暂停释放，增强依赖于增强子的基因转录。值得注意的是，NSD1可作为转录辅激活因子发挥功能，且不依赖于其催化活性。此外，NSD1可激活与索托斯综合征病理生理学相关的发育转录程序，并调控胚胎干细胞（ESC）的多谱系分化。综上，本研究鉴定出NSD1是一类作用于增强子的转录辅激活因子，其参与细胞命运转换与索托斯综合征的发生发展。本研究在经dTAG-13处理0、1和6小时的携带NSD1-dTAG标签的小鼠胚胎干细胞中开展了TT-seq实验。