Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness
Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness
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DOI：
10.1038/s41588-022-01295-6
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发表时间：
2023-01-30
期刊：
影响因子：
30.8
通讯作者：
Rocha, Pedro P.
中科院分区：
文献类型：
--
作者：
Chakraborty, Shreeta;Kopitchinski, Nina;Rocha, Pedro P.
增强子是如何激活其远端靶向启动子的，目前尚不完全清楚。在这里，我们剖析CTCF介导的环是如何促进和限制这种调控相互作用的。利用一系列小鼠的等位基因突变体，我们证明了CTCF既不是Sox2基因与远端增强子相互作用所必需的，也不是其表达所必需的。在Sox2及其远端增强子之间插入各种CTCF基序组合，产生了具有不同程度绝缘的边界，这与转录输出的减少直接相关。然而，在上胚层和神经组织中，增强子接触和转录诱导都不能完全取消，插入未能破坏着床和神经发生。相反，在携带最强边界的突变体的前部未检测到SOX2的表达，并且这些动物在该组织中完全表现出SOX2的缺失。我们认为，具有高密度调控活性的增强子簇可以更好地克服物理障碍，保持忠实的基因表达和表型稳定性。对小鼠Sox2基因座的遗传操作表明，远端增强子激活的基因不需要CTCF介导的环，并且可以跨越异位CTCF介导的边界发生。绕过CTCF边界的能力因其绝缘强度和负责激活的组织特异性增强剂而异。
How enhancers activate their distal target promoters remains incompletely understood. Here we dissect how CTCF-mediated loops facilitate and restrict such regulatory interactions. Using an allelic series of mouse mutants, we show that CTCF is neither required for the interaction of the Sox2 gene with distal enhancers, nor for its expression. Insertion of various combinations of CTCF motifs, between Sox2 and its distal enhancers, generated boundaries with varying degrees of insulation that directly correlated with reduced transcriptional output. However, in both epiblast and neural tissues, enhancer contacts and transcriptional induction could not be fully abolished, and insertions failed to disrupt implantation and neurogenesis. In contrast, Sox2 expression was undetectable in the anterior foregut of mutants carrying the strongest boundaries, and these animals fully phenocopied loss of SOX2 in this tissue. We propose that enhancer clusters with a high density of regulatory activity can better overcome physical barriers to maintain faithful gene expression and phenotypic robustness.Genetic manipulation of the Sox2 locus in mice shows that gene activation by distal enhancers does not require CTCF-mediated loops and can occur across ectopic CTCF-mediated boundaries. The ability to bypass CTCF boundaries varies with their insulation strength and the tissue-specific enhancers responsible for activation.