Contributors:Hannon, Colleen Elizabeth, Wieschaus, Eric F, Molecular Biology Department
In Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into several “affinity” classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classes in vitro and genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by genomic context. Bcd drives an open chromatin state at a subset of its targets. Our data support a model whereby Bcd influences chromatin structure to gain access to low affinity targets at high concentrations, while high affinity targets are found in more accessible chromatin and are bound at low concentrations.
Contributors:Waugh, Aidan, Schedl, Paul
Dosage compensation is a highly conserved process across species that is necessary for correct embryonic development. It is the equalization of transcriptional activation of essential genes across sex-linked chromosomes. In Drosophila melanogaster the Male specific lethal (MSL) complex binds to MSL recognition elements (MRE) within Chromatin entry sites (CES) and spreads to active genes on male the X chromosome and increases transcriptional regulation by 2 fold. Pre-existing arrangement of the CES in space established by long-range interactions between them is necessary for MSL complex recruitment and spreading. By Schedl Lab, an insulator complex LBC was shown to bind to CES. Thus, CES could potentially establish the X chromosome 3D network responsible for MSL binding based on the insulator-like properties of the CES. In this study, I aimed at finding out whether two of the most important CES, roX1 and roX2, exhibit boundary region activity in vivo via transvection assay. I show that the minimal LBC-bound region is insufficient to mediate transvection, and propose that some additional sequences may be required for full boundary function based on the analysis of insulator proteins ChIP-seq data.