Topological Regulation of Gene Expression in the Drosophila Central Nervous System by Megabase-Scale Meta-Loops

Abstract

Genome organization can serve to regulate gene expression at the fundamental level of topologically associating domains (TADs) and tethering elements, but the regulatory function of complex genome organization is poorly understood. Mutations that perturb genomic structure can result in cancer and developmental disorders. Recent studies of the Drosophila central nervous system have unveiled a new level of genome organization called meta-loops, which facilitate TAD pairings through anchor interactions to generate meta-domains. Meta-loops represent the longest regulatory associations to date, yet due to their novelty the role of meta-loops in regulating gene expression remains largely undescribed. In this study, we perturb individual meta-loop anchors within the 3 Mb DIP-numb meta-domain and analyze the effect of the perturbations on gene expression to investigate the role of meta-loops in gene regulation. We demonstrate using ectopic anchor insertions that meta-loops are formed by specific anchor pairings and that meta-loops can foster regulation of a gene by a distal enhancer in a distinct TAD. Meta-loop anchor deletions resulted in lethality, indicating their essential role in gene regulation during development. Our findings shed light on meta-loop anchor specificity and provide evidence supporting the role of meta-loops in gene regulation. The insight generated by this work suggests new mechanisms for how evolution generates novelty in gene expression and how meta-loops influence cell fate determination.