在活细胞中连接组蛋白酰化标记定义的蛋白质组和基因组。

Linking chromatin acylation mark-defined proteome and genome in living cells.

机构信息

Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy of Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Shenzhen Bay Laboratory, Shenzhen 518055, China.

Peking-Tsinghua Center for Life Sciences, Academy of Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing 100871, China.

出版信息

Cell. 2023 Mar 2;186(5):1066-1085.e36. doi: 10.1016/j.cell.2023.02.007.

DOI:10.1016/j.cell.2023.02.007

PMID:36868209

Abstract

A generalizable strategy with programmable site specificity for in situ profiling of histone modifications on unperturbed chromatin remains highly desirable but challenging. We herein developed a single-site-resolved multi-omics (SiTomics) strategy for systematic mapping of dynamic modifications and subsequent profiling of chromatinized proteome and genome defined by specific chromatin acylations in living cells. By leveraging the genetic code expansion strategy, our SiTomics toolkit revealed distinct crotonylation (e.g., H3K56cr) and β-hydroxybutyrylation (e.g., H3K56bhb) upon short chain fatty acids stimulation and established linkages for chromatin acylation mark-defined proteome, genome, and functions. This led to the identification of GLYR1 as a distinct interacting protein in modulating H3K56cr's gene body localization as well as the discovery of an elevated super-enhancer repertoire underlying bhb-mediated chromatin modulations. SiTomics offers a platform technology for elucidating the "metabolites-modification-regulation" axis, which is widely applicable for multi-omics profiling and functional dissection of modifications beyond acylations and proteins beyond histones.

摘要

一种具有可编程位点特异性的可推广策略，用于在未受干扰的染色质上原位分析组蛋白修饰，这仍然是非常需要的，但具有挑战性。本文开发了一种单一位点解析多组学（SiTomics）策略，用于系统绘制动态修饰图谱，并随后对活细胞中特定染色质酰化定义的染色质蛋白组和基因组进行分析。通过利用遗传密码扩展策略，我们的 SiTomics 工具包揭示了短链脂肪酸刺激下的独特的巴豆酰化（例如，H3K56cr）和β-羟基丁酰化（例如，H3K56bhb），并建立了染色质酰化标记定义的蛋白质组、基因组和功能之间的联系。这导致鉴定出 GLYR1 是一种独特的相互作用蛋白，可调节 H3K56cr 的基因体定位，并发现了 bhb 介导的染色质修饰下增强的超级增强子库。SiTomics 为阐明“代谢物-修饰-调控”轴提供了一个平台技术，该技术广泛适用于酰化和组蛋白以外的修饰以及蛋白质以外的多组学分析和功能剖析。