Mesoscale proximity labeling at chromatin to study small molecule mechanism of action [RNAseq_2wk_736]

Proximity labeling traditionally identifies interactomes of a single protein or RNA, though this approach limits mechanistic understanding of biomolecules functioning within complex systems. Here, we demonstrate a strategy for deciphering ligand-induced changes to global biomolecular interactions by enabling proximity labelling at the mesoscale, across an entire cellular system. By inserting nanoscale proximity labelling catalysts throughout chromatin, this system, MesoMap, provided new insights into how HDAC inhibitors regulate gene expression. Furthermore, it revealed that the orphaned drug candidate, SR-1815, regulates disease-linked Syngap1 gene expression through direct inhibition of kinases implicated in both neurological disorders and cancer. Through precise mapping of global chromatin mobility, MesoMap promotes insights into how drug-like chemical probes induce transcriptional dynamics within healthy and disease-associated cellular states. Mouse primary cortical neurons from Syngap1 conditional rescue (Syngap1+/ls) mice were treated with either DMSO (vehicle) or SR-1815 for 2wk and total RNA was collected for sequencing. N=5 for SR-1815 and DMSO.

传统上，邻近标记（proximity labeling）技术仅能鉴定单个蛋白质或RNA的相互作用组（interactome），但该方法限制了我们对复杂系统中行使功能的生物分子的机制性认知。本研究提出一种策略，通过在整个细胞系统的介观尺度（mesoscale）开展邻近标记，解析配体诱导的全局生物分子相互作用变化。通过在染色质（chromatin）全域嵌入纳米级邻近标记催化剂，本研究构建的MesoMap系统为解析组蛋白去乙酰化酶（HDAC）抑制剂如何调控基因表达提供了全新视角。此外，该系统还揭示了孤儿候选药物SR-1815可通过直接抑制与神经系统疾病及癌症均相关的激酶，调控疾病关联基因Syngap1的表达。通过精准绘制全局染色质运动图谱，MesoMap有助于阐明类药化学探针如何在健康及疾病相关细胞状态下诱导转录动态变化。本研究使用Syngap1条件性拯救（Syngap1+/ls）小鼠的原代皮层神经元，分别以二甲基亚砜（DMSO，溶剂对照）或SR-1815处理2周，随后收集总RNA进行测序。SR-1815组与DMSO组的生物学重复数均为N=5。