Chromatin conformation underlying the co-regulation of distal genes by a shared enhancer

Abstract

Gene regulation is critical for normal development and function, but the mechanisms by which it occurs are not fully understood. Recent evidence suggests that long-range promoter-enhancer and promoter-promoter contacts are prevalent throughout metazoan genomes, but their role in regulation remains controversial. Here, we use single-cell fixed imaging methods to examine how chromatin topology varies with gene activity, spatial domain, time, and sequence elements in Drosophila embryos. To explore these questions, we focus on the genes knirps (kni) and knirps-related (knrl), two distal paralogs that are co-regulated in certain domains of the early embryo. We find extensive physical association of these distal genes, in line with prior live imaging studies: despite a 75 kb genomic distance, the promoters are approximately 200 nm apart. Interestingly, the extent of this association varies with gene activity and spatial domain: promoter-promoter distances are smaller in inactive nuclei and nuclei where the two genes are co-regulated, suggesting that chromatin conformation may depend on regulatory state. Adding to this complexity, we find that promoter-promoter distances tighten over developmental time. Finally, we find that promoter-promoter distances increase modestly throughout the entire embryo upon deletion of a newly identified kni tethering element, prompting further questions about the role of sequence elements in mediating long-range promoter- promoter and enhancer-promoter associations.