Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture
Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture
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DOI：
10.1038/s41588-019-0466-z
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发表时间：
2019-08-01
期刊：
影响因子：
30.8
通讯作者：
Ibrahim, Daniel M.
中科院分区：
文献类型：
--
作者：
Despang, Alexandra;Schoepflin, Robert;Ibrahim, Daniel M.
基因组通过依赖于粘连蛋白和 DNA 结合因子 CTCF 的协同作用的过程被组织成称为拓扑关联域 (TAD) 的三维单元。 TAD 的基因组重排已被证明会导致基因错误表达和疾病，但 CTCF 的全基因组缺失对转录没有重大影响。在这里，我们研究了小鼠肢芽中 Sox9-Kcnj2 基因座的体内 TAD 功能。我们发现，去除 TAD 边界和内部的所有主要 CTCF 位点会导致相邻 TAD 的融合，而不会对基因表达产生重大影响。然而，基因错误表达和疾病表型是通过倒置和/或重新定位边界来重定向调控活动来实现的。因此，TAD 结构提供了稳健性和精确性，但对于发育基因调控来说并不是必需的。异常的疾病相关基因激活不是由单纯的绝缘损失引起的，而是需要增强子-启动子接触的 CTCF 依赖性重定向。
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.