Gene neighbourhood integrity disrupted by CTCF loss in vivo

Abstract

The mammalian genome is coiled, compacted and compartmentalized into complex non-random three-dimensional chromatin loops in the nucleus1-3. At the core of chromatin loop formation is CCCTC-binding factor (CTCF), also described as a \"weaver of the genome\"45. Anchored by CTCF, chromatin loops are proposed to form through a loop extrusion process6, organising themselves into gene neighbourhoods2 that harbour insulated enhancer-promoter domains, restricting enhancer activities to genes within loops, and insulating genes from promiscuous interactions outside of loops2,7-9. Studies targeting CTCF binding site deletions at gene neighbourhood boundaries result in localised gene expression dysregulation8,10-12, and global CTCF depletion recently showed CTCF to be crucial for higher hierarchical chromatin organisation of topologically associating domains (TADs)13. However, the role for CTCF in maintaining sub-TAD CTCF gene neighbourhoods and how gene transcription is affected by CTCF loss remains unclear. In particular, how CTCF gene neighbourhoods govern genome-wide enhancer-promoter interactions require clarification. Here, we took an in vivo approach to assess the global dissolution of CTCF anchored structures in mouse cardiomyocyte-specific Ctcf-knockout (Ctcf-KO), and uncovered large-scale ectopic de novo Enhancer-Promoter (E-P) interactions. In vivo cardiomyocyte-specific Ctcf-KO leads to a heart failure phenotype14, but our analysis integrates genome-wide transcription dysregulation with aberrant E-P interactions in context of CTCF-loop structures, identifying how genes engage their E-P interactions, requiring CTCF looping for their maintenance. Our study points to a mammalian genome that possesses a strong propensity towards spontaneous E-P interactions in vivo, resulting in a diseased transcriptional state, manifest as organ failure. This work solidifies the role of CTCF as the central player for specifying global E-P connections.