Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity inDrosophila

Abstract

Cohesin consists of the Smc1-Smc3-Rad21 tripartite ring and the SA protein that interacts with Rad21. The Nipped-B protein loads cohesin topologically around chromosomes to mediate sister chromatid cohesion and facilitate long-range control of gene transcription. It is largely unknown how Nipped-B and cohesin associate specifically with gene promoters and transcriptional enhancers, or how sister chromatid cohesion is established. Here we use genome-wide chromatin immunoprecipitation in Drosophila cells to show that SA and the Fs(1)h (BRD4) BET domain protein help recruit Nipped-B and cohesin to enhancers and DNA replication origins, while the MED30 subunit of the Mediator complex directs Nipped-B and Rad21 to promoters. All enhancers and their neighboring promoters are close to DNA replication origins and bind SA with proportional levels of cohesin subunits. Most promoters are far from origins and lack SA, but bind Nipped-B and Rad21 with sub-proportional amounts of Smc1, indicating that they bind SA-deficient cohesin part of the time. Genetic data confirm that Nipped-B and Rad21 function together with Fs(1)h in vivo to facilitate Drosophila development. These findings demonstrate that Nipped-B and cohesin are differentially targeted to enhancers and promoters and suggest models for how SA and DNA replication help establish sister chromatid cohesion and facilitate enhancer-promoter communication. They indicate that SA is not an obligatory cohesin subunit but a factor that controls cohesin location on chromosomes.

Mechanisms of Interplay between Transcription Factors and the 3D Genome

“…In mESCs, cohesin and its loader Nipbl are found at promoters and enhancers, in addition to CTCF sites (Kagey et al, 2010). In yeast, the RSC chromatin remodeler recruits cohesin loading (Muñoz et al, 2019), while in Drosophila, DNA replication complexes have been implicated (Pherson et al, 2019). Another potential contributor is that the recruitment of RNA polymerase II to active enhancers increases the mobility of those loci, thereby increasing the frequency of longrange contacts (Gu et al, 2018).…”

An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila

“…Interestingly, recent studies have shown that cohesin is required for enhancer activity in mammalian systems, but mainly for long range enhancer activity [77,78]. We find that the 3D genome architecture might play a role in enhancer activity in Drosophila similarly to mammalian system [61].…”

“…Due to the similarities in function of subunits of cohesin and the mediator complex we used a single track for each of the two complexes (Nipped-B for cohesin and MED1 for Mediator) to prevent rules involving cohesin or the mediator complex from becoming diluted across several features. In particular, Nipped-B and SA recruit cohesin to the genome and Rad21 and Smc1 are two cohesion subunits [61]. Fs(1)h was found to recruit Nipped-B [62] and, thus, was also not included in the selected features.…”

“…We used the ChIP-chip datasets generated and pre-processed (M values smoothed over 500 bp) by The modENCODE Consortium for BG3 cell lines [31,32,83,84]. The Nip-pedB ChIP dataset was downloaded from [61]. The full list of datasets used can be found in Additional file 1: Table S2.…”

Insights into HP1a-Chromatin Interactions

“…Several cofactors are also required to establish physical contacts and anchor them to nuclear structures. In Drosophila , proteins such as the modifier of mdg4 (Mod (mdg4)) [ 191 , 192 ] and centrosomal protein of 190kDa (CP190) [ 193 ]; cohesins (like Rad21/Vtd); and condensins (like Cap-H2) are present in different combinations in all types of insulators and fulfill these functions [ 194 ].…”