Nuclear Morphology is Instructed by the Loop Extrusion Program [ChIP-Seq]

More than a century ago Metchnikoff defined neutrophils as small amoeboid-like cells that harbored peculiar polymorphonuclear structures. While since these early studies much has been learned about neutrophil physiology, mechanistic insight into neutrophil polymorphonuclear assembly remains rudimentary. Here we found that depletion of factors, that initiate the loop extrusion program, including NIPBL and MAU2, greatly accelerated the conversion of mononuclear to polymorphonuclear cells and orchestrated the induction of a neutrophil specific transcription signature. Remarkably, mere ablation of either NIPBL or MAU2 expression under conditions that normally prevent neutrophil differentiation, swiftly converted mono-nuclear into polymorphonuclear cells that expressed a neutrophil specific gene program. Depletion of NIPBL and MAU2 in neutrophil progenitors activated an armamentarium of neutrophil-specific enhancers to establish a neutrophil genome depleted for loop extrusion-induced looping. These observations indicate that extinction of the loop extrusion program converts mononuclear progenitor cells into polymorphonuclear cells and suffices to induce a neutrophil specific program of gene expression. Overall design: ChIP-Sequencing for RAD21 in progenitors and NIPBL-depleted progenitors

一个多世纪前，梅契尼科夫（Metchnikoff）将中性粒细胞（neutrophil）定义为一类携带有独特多形核结构的小型阿米巴样细胞。尽管自这些早期研究以来，学界对中性粒细胞生理学已有诸多深入认知，但针对中性粒细胞多形核组装的机制性理解仍较为粗浅。本研究发现，靶向启动环挤出程序（loop extrusion program）的因子（包括NIPBL与MAU2）的敲除，可显著加速单核细胞向多形核细胞的转化，并协同诱导中性粒细胞特异性转录特征。值得注意的是，在通常会抑制中性粒细胞分化的条件下，仅敲除NIPBL或MAU2其中任一因子的表达，即可快速将单核细胞转化为表达中性粒细胞特异性基因程序的多形核细胞。在中性粒细胞祖细胞中敲除NIPBL与MAU2，可激活一套中性粒细胞特异性增强子组合，从而构建出缺乏环挤出介导染色质环的中性粒细胞基因组。上述观测结果表明，终止环挤出程序可将单核祖细胞转化为多形核细胞，且足以诱导中性粒细胞特异性基因表达程序。整体实验设计：对祖细胞及NIPBL敲除祖细胞开展RAD21染色质免疫共沉淀测序（ChIP-Sequencing）。