Project description:Su(Hw) and Shep RIP-seq in Kc and BG3 cell lines RIP-seq with multiple antibodies to two proteins in two Drosophila cell lines, at least 2 replicates for each IP and input
Project description:ChIP-chip experiments with NimbleGen whole-genome tiling arrays to compare Su(Hw), dCTCF, BEAF, and CP190 localization on DNA in Kc and Mbn2 cells revealed that BEAF is a third subclass of CP190-containing insulators. The DNA binding proteins, Su(Hw), dCTCF, and BEAF show unique distribution patterns with respect to the location and expression level of genes, suggesting diverse roles for these three subclasses of insulators in genome organization. Notably, cell line specific localization sites for all three DNA binding proteins as well as CP190 indicate multiple levels at which insulators can be regulated to affect gene expression. Three replicates of Su(Hw), dCTCF, and CP190 ChIP-chip experiments in both Kc and Mbn2 cells as well as two replicates of BEAF ChIP-chip experiments in both Kc and Mbn2 cells were compared.
Project description:ChIP-chip experiments with NimbleGen whole-genome tiling arrays to compare Su(Hw), dCTCF, BEAF, and CP190 localization on DNA in Kc and Mbn2 cells revealed that BEAF is a third subclass of CP190-containing insulators. The DNA binding proteins, Su(Hw), dCTCF, and BEAF show unique distribution patterns with respect to the location and expression level of genes, suggesting diverse roles for these three subclasses of insulators in genome organization. Notably, cell line specific localization sites for all three DNA binding proteins as well as CP190 indicate multiple levels at which insulators can be regulated to affect gene expression.
Project description:Here we compare the distribution of insulator proteins during interphase and mitosis. We performed ChIP-seq analysis on purified populations of interphase and mitotic Kc cells, using antibodies against CP190, dCTCF, BEAF, and Su(Hw).
Project description:Here we examine changes in the distribution of Drosophila insulator proteins during the ecdysone response. We performed ChIP-seq analysis in Kc cells at 0, 3, and 48 hours of ecdysone treatment with antibodies against CP190, Su(Hw), dCTCF, and BEAF-32B.
Project description:Suppressor of Hairy-wing [Su(Hw)] is a globally expressed twelve-zinc finger transcription factor in Drosophila. Su(Hw) is well-known for its role in establishing the gypsy insulator within the gypsy retrotransposon. A direct role of Su(Hw) in gene activation and repression was uncovered through the study in the Drosophila oogenesis, revealing that Su(Hw)-dependent repression of neuronal genes is essential for egg production. Motivated from the spatially restricted expression of Su(Hw) in the testis, we investigated the role of Su(Hw) in spermatogenesis. We discovered that Su(Hw) is required for sperm development and male fertility. Data presented here examined the transcriptional role of Su(Hw) in the Drosophila testis. These studies identified ~400 genes with altered expression in the absence of Su(Hw). Coupled with whole-genome Su(Hw) binding profiles, we identified 145 direct targets of Su(Hw) regulation, of which ~80% show increased transcription upon Su(Hw) loss. Upregulated Su(Hw) targets are enriched for neuronal expression, emphasizing that Su(Hw) represents a functional homolog of mammalian REST that represses neuronal gene expression in non-neuronal tissues.
Project description:Here we compare the distribution of insulator proteins during interphase and mitosis. We performed ChIP-seq analysis on purified populations of interphase and mitotic Kc cells, using antibodies against CP190, dCTCF, BEAF, and Su(Hw). Examination of 4 different insulator proteins during interphase and mitosis
Project description:Here we examine changes in the distribution of Drosophila insulator proteins during the ecdysone response. We performed ChIP-seq analysis in Kc cells at 0, 3, and 48 hours of ecdysone treatment with antibodies against CP190, Su(Hw), dCTCF, and BEAF-32B. Examination of 4 different insulator proteins at 3 time points of ecdysone treatment.
