Dynamic interplay visualized — between enhancer/promoter regions and gene activity

Transcriptional enhancers are short DNA fragments [5 base-pairs (bp) to 25-30 bp] that control gene expression; enhancers can be nearby “upstream” or “downstream”, inside the gene (in an intron that does not get transcribed into the final messenger RNA which then gets translated into the ultimate protein), distant (many thousands of bp of DNA away), and even on a different chromosome from the gene being controlled. It has been at least 35 years since the initial discovery of enhancer modules, but it has been amazing to me –– without distinct visualization –– that the idea of “looping” nearby (cis) or distal (trans) enhancer segments, in order to produce a (contact and) interaction with the promoter (which sits very near the upstream end of the gene) could be so extensively inferred.

A long-standing question in the field remains: how does the physical interaction between enhancers and promoters impact gene expression? Authors [see attached article & editorial] describe an imaging approach by which long-range interactions between promoters and distal enhancers, and their consequences on transcriptional output, can be monitored directly. Transcriptional enhancers in multicellular eukaryotes greatly outnumber genes. In the case of humans, estimates for the total number of enhancers exceed a million elements, compared with the estimated ~21,000 genes. Thus, each promoter-and-gene is, on average, under the control of more than ten regulatory elements.

Authors combined genome-editing and multi-color live imaging to simultaneously visualize (physically) enhancer–promoter interaction and transcription at the single-cell level in Drosophila (fly) embryos. By examining transcriptional activation of a reporter mini-gene by the endogenous even-skipped enhancers –– which are located 150,000 bp away, authors could identify three distinct topological conformational states and could measure their transition kinetics. They demonstrated that sustained proximity of the enhancer to its target is required for activation. Transcription, in turn, affects the three-dimensional topology –– as it enhances the temporal stability of the proximal conformation, and is then associated with further spatial compaction. Moreover, the facilitated long-range activation results in transcriptional competition at the genetic locus, causing corresponding developmental defects. This novel approach offers quantitative insight into the spatial and temporal determinants of long-range gene regulation and their implications for cellular fates. Awesome. Simply awesome.


Nat Genet Oct 2o18; 50: 1296–1303 [article] & pp 1205–1206 [News’N’Views]

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