Mechanisms of Groucho-mediated repression revealed by genome-wide analysis of Groucho binding and activity

Abstract

BackgroundThe transcriptional corepressor Groucho (Gro) is required for the function of many developmentally regulated DNA binding repressors, thus helping to define the gene expression profile of each cell during development. The ability of Gro to repress transcription at a distance together with its ability to oligomerize and bind to histones has led to the suggestion that Gro may spread along chromatin. However, much is unknown about the mechanism of Gro-mediated repression and about the dynamics of Gro targeting.ResultsOur chromatin immunoprecipitation sequencing analysis of temporally staged Drosophila embryos shows that Gro binds in a highly dynamic manner primarily to clusters of discrete (<1 kb) segments. Consistent with the idea that Gro may facilitate communication between silencers and promoters, Gro binding is enriched at both cis-regulatory modules, as well as within the promotors of potential target genes. While this Gro-recruitment is required for repression, our data show that it is not sufficient for repression. Integration of Gro binding data with transcriptomic analysis suggests that, contrary to what has been observed for another Gro family member, Drosophila Gro is probably a dedicated repressor. This analysis also allows us to define a set of high confidence Gro repression targets. Using publically available data regarding the physical and genetic interactions between these targets, we are able to place them in the regulatory network controlling development. Through analysis of chromatin associated pre-mRNA levels at these targets, we find that genes regulated by Gro in the embryo are enriched for characteristics of promoter proximal paused RNA polymerase II.ConclusionsOur findings are inconsistent with a one-dimensional spreading model for long-range repression and suggest that Gro-mediated repression must be regulated at a post-recruitment step. They also show that Gro is likely a dedicated repressor that sits at a prominent highly interconnected regulatory hub in the developmental network. Furthermore, our findings suggest a role for RNA polymerase II pausing in Gro-mediated repression.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3589-6) contains supplementary material, which is available to authorized users.

Loss of TLE3 promotes the mitochondrial program in beige adipocytes and improves glucose metabolism

“…The genomic distribution of TLE3 mapped principally to distal regions of the mouse genome ( Fig. 5C), an observation that is consistent with the TLE/Groucho family being located primarily at enhancers (Chambers et al 2017;Dali et al 2018). There was nearly equal distribution of binding upstream of and downstream from the transcriptional start site (TSS) (Supplemental Fig.…”

Loss of TLE3 Promotes Mitochondrial Program in Beige Adipocytes and Improves Glucose Metabolism

“…The genomic distribution of TLE3 mapped principally to distal regions of the mouse genome ( Figure 5C), an observation that is consistent with the TLE/Groucho family being located primarily at enhancers (37,38). There was nearly equal distribution of binding upstream and downstream of the transcriptional start site (TSS) ( Figure S5A).…”

Collaborative repressive action of the antagonistic ETS transcription factors Pointed and Yan fine-tunes gene expression to confer robustness inDrosophila

“…For example, not only is Pnt essential for proper Yan occupancy, but it also recruits the co-repressor Gro to the same set of regulatory elements. Prior genome-wide analyses of Gro occupancy and function in embryos and cultured cells have shown that Gro-regulated genes are enriched for epigenetic marks and promoter proximal transcripts commonly associated with paused RNA pol II (Kaul et al, 2014;Chambers et al, 2017). Our demonstration of eve de-repression in embryos doubly heterozygous for gro and Trl provides the first genetic evidence of a possible direct mechanistic link between Gro repressive complexes and the RNA pol II pausing machinery.…”