DNA supercoiling restricts the transcriptional bursting of neighboring eukaryotic genes

Abstract

DNA supercoiling has emerged as a major contributor to gene regulation in bacteria. The impact of DNA supercoiling on transcription dynamics in eukaryotes is less clear. Here, using single-molecule dual-color RNA imaging in budding yeast, we show that transcriptional bursting of the divergent and tandem GAL genes is coupled. Upon topoisomerase degradation, supercoils that buildup from transcription inhibit subsequent transcription at neighboring genes, thereby reducing their simultaneous bursting. GAL gene transcription is inhibited more by negative than by positive supercoiling accumulation. Unlike bacteria, wildtype yeast has sufficient topoisomerase levels to minimize inhibition from supercoils at adjacent genes. Overall, we discover fundamental differences in supercoiling-mediated gene regulation between bacteria and yeast and show that rapid supercoiling release in eukaryotes ensures proper gene expression of neighboring genes.One sentence summaryTranscription causes twisting of the DNA double helix, which can inhibit transcription of adjacent genes.

Synthetic analysis of chromatin tracing and live-cell imaging indicates pervasive spatial coupling between genes

“…We predict that if one were able to measure the distances between genes at the initiation of the transcriptional bursts, one should obtain a correlation of ∼.3 if the distance between the promoters of the genes is less than 400 nm. Intriguingly, this level of correlation has been reported between the mRNA levels of adjacent genes in yeast but was attributed to DNA supercoiling (40). Considering the shorter lifetimes of mRNA in yeast, this correlation may be comparable to the nascent RNA in humans.…”

Supercoiling-mediated feedback rapidly couples and tunes transcription

“…We offer testable predictions about the performance of genetic circuits. The predicted changes in reporter output, supercoiling density, and burst dynamics observed in Figures 2 - 4 are experimentally accessible with modern sequencing and single-cell imaging technology ( Guo et al, 2021 ; Mellor et al, 2016 ; Patel et al, 2022 ). Experimental verification of our theoretical results will aid in constructing a mechanistic understanding of how transcription-induced supercoiling couples expression.…”

Supercoiling-mediated feedback rapidly couples and tunes transcription

“…The predicted changes in reporter output, supercoiling density, and burst dynamics observed in figs. 3 and 4 are experimentally accessible with modern sequencing and single-cell imaging technology [38, 54, 55]. Experimental verification of our theoretical results would aid in constructing a mechanistic understanding of how transcription-induced supercoiling couples expression.…”