Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic.

Rachel Waymack,Alvaro Fletcher,Zeba Wunderlich,German Enciso

doi:10.7554/elife.59351

Abstract

Shadow enhancers, groups of seemingly redundant enhancers, are found in a wide range of organisms and are critical for robust developmental patterning. However, their mechanism of action is unknown. We hypothesized that shadow enhancers drive consistent expression levels by buffering upstream noise through a separation of transcription factor (TF) inputs at the individual enhancers. By measuring the transcriptional dynamics of several Kruppel shadow enhancer configurations in live Drosophila embryos, we showed that individual member enhancers act largely independently. We found that TF fluctuations are an appreciable source of noise that the shadow enhancer pair can better buffer than duplicated enhancers. The shadow enhancer pair is also uniquely able to maintain low levels of expression noise across a wide range of temperatures. A stochastic model demonstrated the separation of TF inputs is sufficient to explain these findings. Our results suggest the widespread use of shadow enhancers is partially due to their noise suppressing ability.

Highlights

The first evidence that transcription occurred in bursts, as opposed to as a smooth, continuous process, was observed in Drosophila embryos, where electron micrographs showed that even highly transcribed genes had regions of chromatin lacking associated transcripts between regions of densely associated nascent transcripts (Miller & McKnight, 1979)
We found that the lower expression noise driven by the shadow enhancer pair compared to either duplicated enhancer is a natural consequence of the separation of transcription factor (TF)
If variability in gene expression is driven primarily by fluctuations in upstream factors, the shadow enhancer pair, whose individual enhancers are controlled by different sets of TFs, could provide a form of noise buffering

Summary

Introduction

The first evidence that transcription occurred in bursts, as opposed to as a smooth, continuous process, was observed in Drosophila embryos, where electron micrographs showed that even highly transcribed genes had regions of chromatin lacking associated transcripts between regions of densely associated nascent transcripts (Miller & McKnight, 1979). As visualization techniques have improved, it is increasingly clear that transcriptional bursting is the predominant mode of expression across organisms from bacteria to mammals (Dar, et al.,2012; Sanchez & Golding, 2013; Zenklusen, et al, 2008; Fukaya, et al, 2016) These bursts of transcriptional activity, separated by periods of relative silence, have important implications for cellular function, as mRNA numbers and fluctuations largely dictate these quantities at the protein level (Csardi, et al, 2015; Hansen, et al, 2018). Such fluctuations in regulatory proteins, like TFs and signaling molecules, can propagate down a gene regulatory network, significantly altering the expression levels or noise of downstream target genes (Blake, et al, 2003).

Methods

Results

Conclusion