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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Knockdown of Polyhomeotic in Drosophila Kc cells

ABSTRACT: In this experiment, we used RNAi targeting both copies of the gene polyhomeotic (ph-p and ph-d) to knockdown expression of this factor in Drosophila Kc167 cells. We observed substantial changes to the structure of genomic loci bound by Polycomb-group proteins as assayed by single-molecule based super-resolution imaging with STORM. We also observed a substantial de-repression of many genes which reside in Polycomb-bound domains, as assayed with RNA-seq. mRNA profiles from Drosophila Kc167 cells with and without knockdown the genes ph-p and ph-d were examined in duplicate.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Xiaowei Zhuang

PROVIDER: E-GEOD-75060 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Knockdown of Polyhomeotic in Drosophila Kc cells

Project description:In this experiment, we used RNAi targeting both copies of the gene polyhomeotic (ph-p and ph-d) to knockdown expression of this factor in Drosophila Kc167 cells. We observed substantial changes to the structure of genomic loci bound by Polycomb-group proteins as assayed by single-molecule based super-resolution imaging with STORM. We also observed a substantial de-repression of many genes which reside in Polycomb-bound domains, as assayed with RNA-seq.

2015-11-20 | GSE75060 | GEO

The effects of PTIP on Polycomb mediated repression in Drosophila Kc167 cells.

Project description:Drosophila Kc167 cells were used to test the function of PTIP in regulating gene expression before and after loss of polycomb function. Four condtions were tested using dsRNA knockdowns (RNAi) Experiment Overall Design: Kc167 cells alone, Kc cells with loss of PTIP, cells with loss of polycomb and polyhomeotic, and cells with loss of PTIP, polycomb, and polyhomeotic. Performed in triplicate.

2009-03-15 | E-GEOD-15092 | biostudies-arrayexpress

Polycomb Group proteins are retained at specific sites on chromatin in mitosis

Project description:Epigenetic regulation of gene expression, including by Polycomb Group (PcG) proteins, may depend on heritable chromatin states but how these states can be propagated through mitosis is unclear. Using immunofluorescence and biochemical fractionation, we find PcG proteins associated with mitotic chromosomes in Drosophila S2 cells. Genome-wide sequencing of chromatin immunoprecipitations (ChIP-SEQ) from mitotic cells indicates that Posterior Sex Combs (PSC) and Polyhomeotic (PH) are not present at well-characterized PcG targets including Hox genes in mitosis, but do remain at 11% of their interphase sites. 26% of interphase PSC sites overlap with recently described chromatin domain borders (Sexton et al., 2012), which are genomic regions characterized by low levels of long range contacts. PSC and PH are preferentially retained at these sites in mitosis, including borders flanking both Hox gene clusters. We hypothesize that disruption of long range chromatin contacts in mitosis contributes to PcG protein release from most sites, while persistent binding at sites with minimal long range contacts may nucleate re-establishment of PcG binding and chromosome organization after mitosis. Drosophila S2 cells were colchicine-treated and stained with anti-H3S10p antibody and FACS sorted to give mitotic samples. In parallel asynchronous Drosophila S2 cell cultures were stained for anti-H3 antibody and FACS sorted to give control samples. Chromatin from each of these sorted populations was immunoprecipitated using biotinylated antibodies against PSC. Two replicates of these samples are included. A stable Drosophila S2 cell line expressing biotin-tagged PH was also FACS sorted as above to give mitotic and control samples, and streptavidin-coated beads were used to pulldown biotinlyated PH. Inputs are included for each sample.

2013-01-04 | E-GEOD-38166 | biostudies-arrayexpress

Genome wide analysis of binding of Polyhomeotic and polymerization defective Polyhomeotic in Drosophila S2 cells

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2016-03-08 | E-GEOD-60686 | biostudies-arrayexpress

GAGA Factor maintains promoters in nucleosome-free conformation and allows promoter-proximal pausing [MNase]

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2015-04-04 | E-GEOD-58956 | biostudies-arrayexpress

Two isoforms of Fs(1)h ChIP-seq

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2012-11-15 | E-GEOD-42086 | biostudies-arrayexpress

Characterization of active piRNAs and an piRNA machinery in WRR-1 cells deficient for the Hippo pathway (deficient for the warts tumor suppressor) and expressing activated RasV12 (small RNA)

Project description:We have found that oncogenic Ras combined with loss of the Hippo tumour-suppressor pathway reactivates a primary piRNA pathway in Drosophila somatic cells, coincident with oncogenic transformation. In these cells, Piwi becomes loaded with piRNAs derived from generative loci, which are normally restricted to either the germline or the somatic follicle cells. Negating the pathway leads to increases in the expression of a wide variety of transposons and also to altered expression of some protein coding genes. This correlates with a reduction in the proliferation of the transformed cells in culture, suggesting that at least in this context, the piRNA pathway may play a functional role in cancer. Small RNAs cloned from whole cells, piwi-bound small RNAs and long RNA-Seq were performed in wts-RNAi;RasV12 cells to identify piRNAs and gene expression and compared to RasV12 cells, somatic OSS cells, and germline UAS-wts-RNAi;UAS-RasV12 control ovaries. After knock-down of several components of the piRNA machinery in WRR-1 cells (piwi, zuchini, armitage, aubergine, argonaute3) and GFP and/or dsRED control knock-downs, small RNAs were cloned and gene expression profiles (RNA-Seq) were established.

2016-08-01 | E-GEOD-83871 | biostudies-arrayexpress

ChIP-seq mapping of Drosophila TFIIIC (dTFIIIC220; CG7099) and SMC containing complexes in Kc167 cells

Project description:We map the genome-wide binding profiles for dTFIIIC220, as well as the Drosophila cohesin and condensin complexes in the late-stage embryonic cell line Kc167 Examination of several proteins in the Kc167 cell line

2014-05-14 | E-GEOD-54529 | biostudies-arrayexpress

Histone Phosphoacetylation ChIP-seq of Kc167 cells from Drosophila

Project description:ChIP-seq was performed using Drosophila Kc167 cells using antibodies against H3K4me3 to identify active promoters and H3K4me1 to identify active enhancers. H3K27ac ChIPseq was performed to identify active promoters and enhancers. Once enhancers and promoters were identified, JIL-1 and histone phosphorylation, H3K9acS10ph and H3K27acS28ph, ChIP-seq was performed to look at binding trends. JIL-1 and phosphoacetlation is found at low levels at inactive enhancers and shows increase at active enhancers and promoters. Here we examine histone phosphorylation by JIL-1 and acetylation of H3K27ac by CBP at transcriptionally active vs. inactive promoters and enhancers. ChIP-seq is performed in Kc167 Drosophila cells using antibodies against JIL-1, H3K27acS28ph, H3K9acS10ph, H3K4me3, H3K4me1, and H3K27ac.

2012-03-29 | E-GEOD-36374 | biostudies-arrayexpress

TAP-ORC2 and control ChIP experiments in Drosophila Kc167 cells

Project description:Expression data from Kc167 cells under normal conditions. Used to assess expression levels of genes with ORC bound at promoter. Control experiments in support of our previous modencode submssion GSE17282. Kc167 cells were harvested from log phase gorwth. RNA extraction and hybridization on Affymetrix microarrays. Chromatin immunoprecipitation with IgG against TAP-ORC2 or control cells.

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