Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE118484 | GEO | 2019/02/20
REPOSITORIES: GEO
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Project description:Effects of Nipped-B and Rad21 sister chromatid cohesin proteins on gene expression data in ML-DmBG3 cells derived from Drosophila melanogaster larval central nervous system We examined the effects of Nipped-B and Rad21 knockdown on gene expression in BG3 cells using microarrays that measure over 18,700 transcripts to (a) determine if the effects of cohesion on E(spl)-C and invected-engrailed expression are unique, (b) look for effects of cohesin on regulators of E(spl)-C and engrailed, and (c) obtain a comprehensive view of the effects of cohesin on gene expression.
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Project description:The cohesin complex has crucial roles in many structural and functional aspects of chromosomes including sister chromatid cohesion, genome organization, gene transcription and DNA repair. Cohesin recruitment onto chromosomes requires nucleosome free DNA and a specialized cohesin loader complex comprised of the Scc2 and Scc4 subunits. The cohesin loader, in addition to stimulating cohesin ATP hydrolysis and facilitating topological loading onto DNA, leads cohesin to chromatin receptors such as the RSC chromatin remodeling complex. Here, we explore the cohesin loader-RSC interaction and show that its Scc4 subunit contacts a conserved RSC ATPase motor module. The cohesin loader enhances RSC chromatin remodeling activity in vitro, as well as promoter nucleosome eviction in vivo. These findings provide insight into how the cohesin loader recognizes, as well as influences, the chromatin landscape, with implications for our understanding of human developmental disorders including Cornelia de Lange and Coffin-Siris syndromes.
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Project description:Effects of Nipped-B and Rad21 sister chromatid cohesin proteins on gene expression data in ML-DmBG3 cells derived from Drosophila melanogaster larval central nervous system; We examined the effects of Nipped-B and Rad21 knockdown on gene expression in BG3 cells using microarrays that measure over 18,700 transcripts to (a) determine if the effects of cohesion on E(spl)-C and invected-engrailed expression are unique, (b) look for effects of cohesin on regulators of E(spl)-C and engrailed, and (c) obtain a comprehensive view of the effects of cohesin on gene expression. Experiment Overall Design: Effects of cohesin knockdown on E(spl)-C and invected-engrailed transcription vary over time, so we used two independent samples for three days after RNAi treatment, one four day and one six day sample for both Nipped-B and Rad21 knockdown, and mock RNAi controls for each time point. Experiment Overall Design: For RNAi treatment, cells were plated at 5x106 cells per 3 cm well. Media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, and 10 micrograms per ml insulin. The indicated amount of dsRNA was added per well. Media was adjusted to 3 ml and 10% FCS with Schneiderâs media after 2 hrs. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA templates using primers with T7 promoters (see supplementary file linked below). Equal amounts of two dsRNAs against each target were used.
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