Topological isolation as a mechanism for precise control of developmental regulators in mammalian genomes [RNA-seq]

Recent investigation of insulated chromosome structures suggests their crucial role in controlling proper gene expression. However, it remains unclear whether developmental regulators can be precisely controlled by such insulated structures and whether developmental failure is caused by disrupting the structure boundaries. Here we identified topologically insulated regions (TIRs) from deeply sequenced human embryonic stem cell (hESC) Hi-C data and analyzed the gene distribution across TIRs. We find a notable enrichment of developmental regulators isolated from other genes by TIRs and show that the boundary CTCF sites are highly conserved across species. Perturbation of such boundaries in hESCs leads to failure to properly differentiate. Enhancer activity is restricted by such boundaries, further pointing towards their regulatory importance. Finally, germline mutations affecting such boundaries are subject to purifying selection and are underrepresented in the human population. Our findings provide new insights into mammalian genome organization and suggest a possible role of gene insulation through chromosomal folding structures for precise control of developmental regulators.

近期针对染色质绝缘结构的研究表明，其在调控基因正确表达过程中发挥着至关重要的作用。然而，目前仍存在两个尚未明确的科学问题：其一，发育调控因子能否通过此类绝缘结构实现精准调控；其二，发育失败是否由结构边界的破坏所引发。本研究从深度测序的人类胚胎干细胞（human embryonic stem cell, hESC）Hi-C数据中鉴定得到拓扑绝缘区域（topologically insulated regions, TIRs），并分析了基因在各TIR间的分布特征。研究发现，被TIRs与其他基因分隔开的发育调控因子存在显著富集现象，同时证实边界CTCF结合位点在跨物种间具有高度保守性。在hESC中扰动此类边界会导致细胞无法正常分化。增强子的活性会受到此类边界的限制，进一步印证了其在基因调控中的重要性。最后，影响此类边界的生殖系突变会受到纯化选择的作用，且在人类人群中所占比例偏低。本研究结果为哺乳动物基因组组织结构研究提供了全新视角，同时表明通过染色质折叠结构实现的基因绝缘，可能在发育调控因子的精准调控中发挥关键作用。