Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes [ChIP-seq]. Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes [ChIP-seq]

STAG2 encodes a cohesin component and is frequently mutated in myeloid neoplasms, showing highly significant co-mutation patterns with other drivers, including RUNX1. However, the molecular basis of cohesin-mutated leukemogenesis remains poorly understood. Here we show a critical role of an interplay between Stag2 and Runx1 in the regulation of enhancer-promoter looping and transcription in hematopoiesis. Combined loss of Stag2 and Runx1, which co-localize at enhancer-rich, Ctcf-deficient sites, synergistically attenuates enhancer-promoter loops, particularly at sites enriched for RNA polymerase II and Mediator, and deregulates gene expression, leading to myeloid-skewed expansion of hematopoietic stem/progenitor cells (HSPCs) and myelodysplastic syndromes (MDS). Attenuated enhancer-promoter loops in Stag2/Runx1-deficient cells are associated with downregulation of genes with high basal transcriptional pausing, which are important for the regulation of HSPCs. Down-regulation of high-pausing genes is also confirmed in STAG2/cohesin-mutated primary AML/MDS samples. Our results highlight a unique STAG2/RUNX1 interplay in gene regulation and provide insights into cohesin-mutated leukemogenesis. Overall design: Comprehensive epigenome sequencing (RNA-seq, ATAC-seq, ChIP-seq and Hi-C) in WT, Stag2 knockout, Runx1 knockout, and double knockout cells.

STAG2 基因编码黏连蛋白（cohesin）复合物的一个组分，在髓系肿瘤中频发突变，并与包括RUNX1在内的其他驱动基因存在极具统计学意义的共突变模式。然而，黏连蛋白突变介导的白血病发生的分子机制仍未被充分阐明。本研究揭示了Stag2与Runx1之间的相互作用在造血过程中增强子-启动子环化与转录调控中的关键作用。共定位于富含增强子且CTCF（Ctcf）缺失区域的Stag2与Runx1同时缺失，会协同减弱增强子-启动子环化作用，尤其是在RNA聚合酶II（RNA polymerase II）和中介体复合物（Mediator）富集的区域，并导致基因表达失调，最终引发造血干/祖细胞（hematopoietic stem/progenitor cells, HSPCs）的髓系偏态扩增以及骨髓增生异常综合征（MDS）。Stag2/Runx1缺失细胞中减弱的增强子-启动子环化，与调控造血干/祖细胞至关重要的高基础转录暂停基因的表达下调存在关联。在STAG2/黏连蛋白突变的原发性急性髓系白血病（AML）/骨髓增生异常综合征样本中，也证实了高暂停基因的表达下调。本研究结果凸显了STAG2/RUNX1相互作用在基因调控中的独特性，并为阐释黏连蛋白突变介导的白血病发生机制提供了新的研究视角。实验设计：对野生型（WT）、Stag2基因敲除、Runx1基因敲除以及双基因敲除的细胞开展全表观基因组测序，涵盖RNA测序（RNA-seq）、转座酶可及性测序（ATAC-seq）、染色质免疫共沉淀测序（ChIP-seq）以及高通量染色体构象捕获测序（Hi-C）。