The Snail Repressor Inhibits Release, Not Elongation, of Paused Pol II in the Drosophila Embryo

Abstract

SUMMARY The development of the precellular Drosophila embryo is characterized by exceptionally rapid transitions in gene activity, with broadly distributed maternal regulatory gradients giving way to precise on/off patterns of gene expression within a one hour window, between 2 and 3 hrs after fertilization [1]. Transcriptional repression plays a pivotal role in this process, delineating sharp expression patterns (e.g., pair-rule stripes) within broad domains of gene activation. As many as 20 different sequence-specific repressors have been implicated in this process, yet the mechanisms by which they silence gene expression have remained elusive [2]. Here we report the development of a method for the quantitative visualization of transcriptional repression. We focus on the Snail repressor, which establishes the boundary between the presumptive mesoderm and neurogenic ectoderm [3]. We find that elongating Pol II complexes complete transcription after the onset of Snail repression. As a result, moderately sized genes (e.g., the 22 kb sog locus) are fully silenced only after tens of minutes of repression. We propose that this “repression lag” imposes a severe constraint on the regulatory dynamics of embryonic patterning, and further suggest that post-transcriptional regulators, like microRNAs, are required to inhibit unwanted transcripts produced during protracted periods of gene silencing.

Mitosis-associated repression in development

“…Prior studies with fixed embryos suggest that these enhancers respond to different levels of the Snail repressor (e.g., see Bothma et al 2011). The brk 5 ′ enhancer appears to be more efficiently repressed by Snail as compared with the sog intronic enhancer.…”

Complex cis-regulatory landscape of the insulin receptor gene underlies the broad expression of a central signaling regulator

“…S10 and Table S3 Why do genes, such as the insulin receptor, span substantial genomic regions? One observation relating to developmental gene expression is that genes harboring large introns demonstrate substantially different regulatory kinetics, whereby the traversing of extra genomic distance necessarily introduces a lag in induction and repression (Arnosti, 2011;Bothma et al, 2011). Although this effect might play a role in InR expression as well, it is clear that the intronic sequences of the gene serve a role that is far more complex than that of a simple spacer; we find that the transcribed space of the gene contains multiple regulatory elements that provide both redundant as well as contrasting regulatory output, some in a cellspecific manner (Fig.…”

RNA polymerase II pausing during development

“…Genome-wide binding of the zinc finger repressor Snail, for instance, was found to correlate with paused Pol II . This suggests that transcriptional repressors can block the release of Pol II (Bothma et al, 2011). To do so, repressors may act locally at enhancers to prevent adjacent activators from stimulating Pol II pause release at the promoter (also called 'quenching' or short-range repression).…”