Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness

FARE Award Winner

Authors

• K Canubas
• M Xu
• WK Kelly
• J Marte
• HA Sater
• JL Gulley
• W Lassoued

Abstract

Transcriptional control by distal regulatory elements called enhancers is an integral feature of gene regulation. CTCF-mediated chromatin loops play a crucial role in facilitating interactions between distal genomic regions. However, the in vivo significance of this model is poorly understood. To explore how enhancer-promoter interactions arise and assess the impact of disrupting 3D chromatin structure on gene expression, we generated an allelic series of mouse mutants that perturb the structure of the Sox2 locus. We show that in the epiblast and in neuronal tissues, CTCF-mediated loops are neither required for the interaction of the Sox2 promoter with distal enhancers, nor for its expression. Insertion of various combinations of CTCF motifs between Sox2 and its distal enhancers generated ectopic loops with varying degrees of insulation that directly correlated with reduced transcriptional output. Yet mutants exhibiting strongest insulation, with six CTCF motifs in divergent orientation, could not fully abolish activation by enhancers, and failed to disrupt implantation and neurogenesis. In contrast, cells of the anterior foregut were more susceptible to chromatin structure disruption with no detectable SOX2 expression in mutants with the strongest CTCF-mediated boundaries. These animals phenocopied loss of SOX2 in the anterior foregut, failed to separate trachea from esophagus and died perinatally. We propose that baseline transcription and enhancer density may influence the tissue-specific ability of distal enhancers to overcome physical barriers and maintain faithful gene expression during embryonic development. Our work suggests that enhancer-promoter interactions that can overcome chromosomal structural perturbations, play an essential role in maintaining phenotypic robustness.

Scientific Focus Area: Genetics and Genomics

This page was last updated on Monday, September 25, 2023