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.
Highlights
The transcriptional corepressor Groucho (Gro) is required for the function of many developmentally regulated DNA binding repressors, helping to define the gene expression profile of each cell during development
Support for this model comes from the following observations: (1) Gro forms tetramers and higher order oligomers and repression can be compromised by mutations that prevent oligomerization [9,10,11,12,13]; (2) Gro recruits the histone deacetylase Rpd3 resulting in histone hypoacetylation and Gro function can be compromised by Rpd3 mutations and by histone deacetylase inhibitors [14,15,16,17,18]; and (3) Gro binds to hypoacetylated histone tails [19, 20]
Gro is transiently recruited to thousands of sites in the developing embryo Using a validated affinity purified polyclonal antibody raised against the Gro GP domain (Additional file 3: Figure S1A), Gro chromatin immunoprecipitation sequencing (ChIP-seq) was performed on fly embryos collected during three successive 2.5 h timespans collectively encompassing 1.5 to 9 h of development
Summary
The transcriptional corepressor Groucho (Gro) is required for the function of many developmentally regulated DNA binding repressors, helping to define the gene expression profile of each cell during development. Gro-mediated repression is not clearly understood, one possibility is that Gro spreads along chromatin fibers to generate large transcriptionally silent domains. Support for this model comes from the following observations: (1) Gro forms tetramers and higher order oligomers and repression can be compromised by mutations that prevent oligomerization [9,10,11,12,13]; (2) Gro recruits the histone deacetylase Rpd resulting in histone hypoacetylation and Gro function can be compromised by Rpd mutations and by histone deacetylase inhibitors [14,15,16,17,18]; and (3) Gro binds to hypoacetylated histone tails [19, 20]. Loss of the ability to oligomerize failed to decrease median peak widths significantly, it did result in the identification of fewer Gro-associated regions [22]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
