Nuclear IDH1 regulates human erythropoiesis by eliciting chromatin state reprogramming

Although, IDH1 has been recognized to play critical roles in the regulation of dynamic chromatin states, the mechanism remained largely unknown. Here, using the human erythropoiesis system, we presented an innovative perspective of metabolism independent role of nuclear IDH1. We discovered that IDH1 acted as a nuclear located chromatin-binding protein. Knockdown of IDH1 induced chromatin reorganization and subsequently aroused aberrant biological events germination on erythroid precursors in a metabolism independent manner. IDH1 knockdown induced genome-wide coordinate changes in the distribution and intensity of multiple histone marks, among which H3K79me3 was identified to be the decisive factor in chromatin state reprogramming. Integrating ChIP-seq, ATAC-seq and RNA-seq recognized SIRT1 to be the key gene affected by IDH1 deficiency. Taken together, these findings provided a novel insight for further clarifying the fundamental biological function of IDH1 which had substantial implications for an in-depth understanding of the pathogenesis of diseases with IDH1 dysfunction and accordingly the development of therapeutic strategies. Overall design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K79me3, H3K9me3 and H3K27me2 in erythroid cells

尽管异柠檬酸脱氢酶1（IDH1）已被证实可调控动态染色质状态并发挥关键作用，但其具体分子机制在很大程度上仍未明确。本研究以人类红细胞生成系统为模型，揭示了核定位IDH1具备不依赖代谢通路的独立功能这一创新性见解。研究发现，IDH1作为核定位的染色质结合蛋白发挥功能。敲低IDH1可诱导染色质发生重构，并以不依赖代谢的方式，引发红系前体细胞中异常生物学事件的产生。IDH1敲低会引发全基因组范围内多种组蛋白修饰的分布与强度出现协同变化，其中组蛋白H3第79位赖氨酸三甲基化（H3K79me3）被证实是染色质状态重编程的决定性调控因子。通过整合染色质免疫共沉淀测序（ChIP-seq）、转座酶可及性染色质测序（ATAC-seq）与RNA测序（RNA-seq）的数据，研究确认SIRT1是受IDH1缺失影响的关键靶基因。综上，本研究的发现为进一步阐明IDH1的基础生物学功能提供了全新的研究视角，这对于深入理解IDH1功能异常相关疾病的发病机制，并据此开发针对性治疗策略具有重要意义。整体实验设计：针对红系细胞中的组蛋白H3第79位赖氨酸三甲基化（H3K79me3）、组蛋白H3第9位赖氨酸三甲基化（H3K9me3）及组蛋白H3第27位赖氨酸二甲基化（H3K27me2）开展染色质免疫共沉淀测序（ChIP-seq）。