Nuclear Morphology is Instructed by the Loop Extrusion Program [RNA-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. Performed gene expression profiling by RNA-seq in progenitors and differentiated neutrophils. Overall design: We performed RNA-seq of NIPBL, MAU2, and both NIPBL-MAU2 depleted progenitors as well as differentiated neutrophils for gene expression profiling analysis.

一个多世纪前，梅契尼科夫将中性粒细胞（neutrophil）定义为一类小型类阿米巴样细胞，其拥有独特的多叶核结构。尽管自这些早期研究以来，学界对中性粒细胞的生理特性已有诸多认知，但针对中性粒细胞多叶核组装的机制性理解仍较为粗浅。本研究发现，敲除启动环挤出（loop extrusion）程序的相关因子（包括NIPBL与MAU2），可显著加速单核细胞向多叶核细胞的转化，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培养条件下，仅敲除NIPBL或MAU2其中任一基因的表达，即可快速将单核核细胞转化为表达中性粒细胞特异性基因程序的多叶核细胞。在中性粒细胞祖细胞中敲除NIPBL与MAU2，可激活整套中性粒细胞特异性增强子，进而在中性粒细胞基因组中消除环挤出介导的染色质环形成。上述研究结果表明，终止环挤出程序即可将单核核祖细胞转化为多叶核细胞，且足以诱导中性粒细胞特异性基因表达程序。本研究通过RNA测序（RNA-seq）对祖细胞与分化成熟的中性粒细胞开展了基因表达谱分析。整体实验设计：为开展基因表达谱分析，本研究对敲除NIPBL、MAU2以及同时敲除NIPBL与MAU2的祖细胞，以及分化成熟的中性粒细胞进行了RNA测序。