RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.
Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.
Nat Genet. 2019 Aug;51(8):1263-1271. doi: 10.1038/s41588-019-0466-z. Epub 2019 Jul 29.
The genome is organized in three-dimensional units called topologically associating domains (TADs), through a process dependent on the cooperative action of cohesin and the DNA-binding factor CTCF. Genomic rearrangements of TADs have been shown to cause gene misexpression and disease, but genome-wide depletion of CTCF has no drastic effects on transcription. Here, we investigate TAD function in vivo in mouse limb buds at the Sox9-Kcnj2 locus. We show that the removal of all major CTCF sites at the boundary and within the TAD resulted in a fusion of neighboring TADs, without major effects on gene expression. Gene misexpression and disease phenotypes, however, were achieved by redirecting regulatory activity through inversions and/or the repositioning of boundaries. Thus, TAD structures provide robustness and precision but are not essential for developmental gene regulation. Aberrant disease-related gene activation is not induced by a mere loss of insulation but requires CTCF-dependent redirection of enhancer-promoter contacts.
基因组通过一个依赖于黏合蛋白(cohesin)和 DNA 结合因子 CTCF 协同作用的过程，组织成称为拓扑关联域 (TADs) 的三维单元。已经表明 TAD 的基因组重排会导致基因表达错误和疾病，但 CTCF 的全基因组耗竭对转录没有明显影响。在这里，我们在 Sox9-Kcnj2 基因座的小鼠肢芽中体内研究 TAD 的功能。我们表明，边界和 TAD 内所有主要 CTCF 位点的缺失导致相邻 TAD 融合，而对基因表达没有重大影响。然而，通过反转和/或边界重新定位来重新引导调控活性，实现了基因表达错误和疾病表型。因此，TAD 结构提供了稳健性和精确性，但对于发育基因调控并非必不可少。异常的疾病相关基因激活不是仅仅由于失去了绝缘而引起的，而是需要 CTCF 依赖性的增强子-启动子接触的重新定向。
