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Drosophila melanogaster

ABSTRACT: Transcriptome analysis upon overexpression of SIN3 187HA in Drosophila cultured cells

PROVIDER: PRJNA294314 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2173472_1.fastq.gz	Fastqsanger.gz
	SRR2173472_2.fastq.gz	Fastqsanger.gz
	SRR2173473_1.fastq.gz	Fastqsanger.gz
	SRR2173473_2.fastq.gz	Fastqsanger.gz
	SRR2173474_1.fastq.gz	Fastqsanger.gz

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Drosophila melanogaster

Project description:Transcriptome analysis upon SIN3 or dKDM5/LID knockdown or both under normal and paraquat induced stress conditions in Drosophila S2 cultured cells

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Transcriptome analysis upon SIN3 or dKDM5/LID knockdown or both under normal and paraquat induced stress conditions in Drosophila S2 cultured cells

Project description:SIN3 the scaffold protein of a histone deacetylase complex interacts with a histone demethylase KDM5 (little imaginal discs - LID) in Drosophila. Reduction of SIN3 or dKDM5/LID both result in similar phenotypes during cell proliferation and wing development. To identify underlying transcriptional changes that may contribute to these phentypic defects we performed whole genome expression analysis in Drosophila cultured cells upon RNAi-mediated knockdown of Sin3A, lid or both. We identified a large number of genes regulated by SIN3, dKDM5/LID or both. While many common genes were regulated by SIN3 and dKDM5/LID an enrichment for genes involved in stress tolerance pathways was observed. Additional RNAseq analysis of expression changes upon knockdown of Sin3A, lid or both under paraquat mediated oxidative stress conditions identified significant changes in genes involved in cell cycle related processes.

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Transcriptome analysis upon SIN3 or dKDM5/LID knockdown or both under normal and paraquat induced stress conditions in Drosophila S2 cultured cells

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Project description:Mapping binding sites of SIN3 isoforms across the Drosophila genome.

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Mapping binding sites of SIN3 isoforms across the Drosophila genome.

Project description:SIN3 associates with RPD3 and other accessory proteins to form the SIN3 histone modifying complex. A single Sin3A gene encodes multiple SIN3 isoforms, of which SIN3 187 and SIN3 220 are predominant. Previous studies from our laboratory and others have indicated that SIN3 isoforms play non-redundant roles during fly development, however, the genes regulated by SIN3 isoforms are not known. We mapped the genome-wide binding sites of SIN3 isoforms in Drosophila. We established stable S2 cell lines that express either HA-tagged SIN3 187 or SIN3 220. The binding profiles revealed that the majority of the binding sites of SIN3 isoforms are overlapping. Our data revealed that SIN3 isoforms localize to euchromatic regions of the genome and enrichment of SIN3 isoforms are generally concentrated around the transcription start sites of genes. In addition, the extent of SIN3 binding confirmed previous findings indicating that SIN3 is a global transcriptional regulator. Genome-wide binding analysis of SIN3 187 and SIN3 220 in Drosophila. Using chromatin prepared from cell lines expressing either of the isoforms, we performed chromatin immunoprecipitation on chromatin prepared from cells that expresses either of the isoforms using an antibody against HA (ChIP). We coupled our ChIP with high resolution deep sequencing (ChIP-seq) to identify genomic targets of SIN3 isoforms.

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