Characterization of the spatiotemporal architecture of the genome and its relevance to biological function

Abstract

A variety of cis-regulatory elements govern the spatial organization of chromatin. The exact cause and consequence of this organization with respect to transcriptional activity remains elusive. Here we present an approach based on multi-color imaging to discriminate the specificity of various cis-regulatory elements in establishing and maintaining discrete chromosomal configurations at the single cell level. Specifically, targeting a locus with multiple enhancers driving expression in distinct spatial domains, we simultaneously measure the position of these elements inside and outside of their domains of control. We observe the median distance between an enhancer and active promoter is approximately 160 nm. Interestingly, distances between enhancer-promoter pairs are larger (170-220 nm) in transcribing domains in which the tagged enhancer is not actively driving transcription. This is in contrast to inactive domains which all demonstrate a relatively compact organization with median distances ranging from 120-160 nm, suggesting that transcription causes a local decompaction in conjunction with sustained enhancer-specific proximity. The magnitude of these distances is too large, however, to imply that there is sustained direct contact. To further characterize the dynamics of specific enhancer-promoter interactions we designed a system to track both the position and activity of genes and their regulatory elements in vivo. We are able to observe insulator-mediated enhancer-promoter interactions across genomic separations ranging from 47 kb to 568 kb. Surprisingly, we also observed unassisted enhancer-promoter interactions at genomic distances of > 70 kb which cease to exist at over 140 kb. Leveraging the dynamic information present in this data, we observed complex and dynamic interactions between transcription, spatial configurations, and their respective temporal stability, with potential functional consequences for the course of development.