Non-coding loci without epigenomic signals can be essential for maintaining global chromatin organization and cell viability [single-cell RNA-seq]

Most non-coding regions of the human genome do not harbour any annotated element and are even not marked with any epigenomic or protein binding signal. However, an overlooked aspect of their possible role in stabilizing 3D chromatin organization has not been extensively studied. To illuminate their structural importance, we started with the non-coding regions forming many 3D contacts (referred to as hubs) and performed a CRISPR library screening to identify dozens of hubs essential for cell viability. Hi-C and single cell transcriptomic analyses showed that their deletion could significantly alter chromatin organization and impact the distal genes expression. This study revealed the 3D structural importance of non-coding loci that are not associated with any functional element, providing a new mechanistic understanding of disease-associated genetic variations (GVs), and we focused on single nucleotide variations. Furthermore, our analyses also suggest a powerful approach to develop "one-drug-multiple-targets" therapeutics targeting disease-specific non-coding regions. Examination of gene expression profile of K562 hub_22_7 deletion cells at single cell level

人类基因组的绝大多数非编码区域既未注释任何功能元件，也未被任何表观基因组（epigenomic）信号或蛋白质结合信号所标记。然而，其在稳定三维染色质（3D chromatin）组织中可能发挥的作用这一被忽视的研究方向，尚未得到广泛探索。为阐明这些区域的结构重要性，我们以形成大量三维染色质相互作用的非编码区域（下称枢纽（hubs））为研究对象，通过CRISPR文库筛选鉴定出数十个对细胞存活至关重要的枢纽区域。Hi-C技术与单细胞转录组学分析结果显示，敲除这些枢纽区域可显著改变染色质组织结构，并影响远端基因的表达。本研究揭示了未与任何功能元件相关联的非编码基因座的三维结构重要性，为理解疾病相关遗传变异（GVs）提供了全新的机制视角，且本研究聚焦于单核苷酸变异（single nucleotide variations）。此外，我们的分析还提出了一种极具潜力的策略，可用于开发针对疾病特异性非编码区域的"one-drug-multiple-targets"疗法。本研究对K562细胞中hub_22_7区域敲除细胞开展了单细胞水平的基因表达谱分析。