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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.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE75060 | GEO | 2015/11/20

SECONDARY ACCESSION(S): PRJNA302312

REPOSITORIES: GEO

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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. mRNA profiles from Drosophila Kc167 cells with and without knockdown the genes ph-p and ph-d were examined in duplicate.

2015-11-20 | E-GEOD-75060 | biostudies-arrayexpress

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

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

Project description:To understand the role of the conserved Sterile Alpha Motif of the Polycomb Group protein Polyhomeotic, the genome wide distribution of wild type and polymerization defective Polyhomeotic containing mutations in the SAM domain was determined by ChIP-SEQ. ChIP-seq Identification of polyhomeotic wild type (PH-WT) and mutant (PH-ML) binding sites.

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

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

2016-03-08 | GSE60686 | GEO

Time course of response of Kc cells to ecdysone

Project description:The changes in transcript titers are described for Drosophila Kc167 cells following 5-48 hr treatment with 20-hydroxyecdysone. Keywords: hormone response

2009-03-20 | GSE10926 | GEO

MRG15_Q2481.Kc

Project description:modENCODE_submission_3046 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of 125 chromosomal proteins across For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Cell Line Kc167; Antibody MRG15 Q2481 (target is MRG15)

2010-11-18 | E-GEOD-25366 | biostudies-arrayexpress

Chemical footprinting of Polyhomeotic-proximal1289-1577

Project description:The Polycomb protein Polyhomeotic (Ph) is implicated in organizing chromatin to regulate gene expression. This activity depends on the sterile alpha motif in Ph, which can form helical polymers. This polymerization activity is believed to create macromolecular assemblies of Polycomb proteins and chromatin in cells. To understand how this may occur, and the possible role of phase separation in the process, we analyzed a truncated version of Ph (aa1289-1577, Mini-Ph) in vitro. We find that Mini-Ph forms phase separated condensates with DNA or chromatin in vitro. To understand how Ph SAM polymerization contributes to this activity, and how Mini-Ph conformation might change on binding DNA and phase separating, we used a protein footprinting method based on chemical acetylation of accessible lysine residues. Mini-Ph or a polymerization mutant, alone, or with DNA, was treated with sulfo-NHS-acetate to acetylate accessible lysines. After protein denaturation, the protein was treated with propionic acid to propionylate unacetylated lysines. Samples were analyzed by MS, and the ratio of acetylated/propionylated lysines quantified at each position using MaxQuant.

2020-07-10 | MSV000085717 | MassIVE

Ecdysone Response Timecourse in Kc Cells

Project description:Kc167 Cells were plated at 0.5x106/ml and grown at 23.50C. They were treated with 20-HE (Sigma) at a final concentration of 5x10-7M. The reference sample was total RNA isolated at 0 hr. after treatment. The experimental samples were total RNA isolated from cells treated for 1, 3, 6, 12, 24, and 48 hours.

2008-06-12 | GSE11625 | GEO

An intrinsic tumor-suppression mechanism mediated by steroid hormone in Drosophila

Project description:Polycomb group (PcG) proteins are evolutionarily conserved epigenetic regulators that mediate histone modifications and suppress target gene expression, therefore establish and maintain cellular memory during development1-3. Deregulation of PcG genes is associated with various human cancers, but the mechanisms are incompletely understood4. Polyhomeotic (Ph), one of the Drosophila PcG proteins, can act as a tumor suppressor in larval imaginal discs5, 6. Cells mutant for ph overgrow and give rise to neoplastic tumors during larval development6. Here we report an intrinsic tumor-suppression mechanism mediated by the steroid hormone ecdysone in Drosophila. During metamorphosis, ecdysone transforms tumorigenic ph mutant cells into non-tumorigenic cells, thereby suppressing the malignant growth in adult flies. We demonstrate ecdysone exerts its function by inducing the expression of microRNA lethal-7 (let-7), which suppresses its target gene chinmo, to inhibit the tumorigenic growth of ph mutant cells. Furthermore, we show let-7 can also suppress the overgrowth of brain tumors in brain tumor (brat) mutant flies, indicating this intrinsic mechanism is functional in different tissues to suppress neoplastic growth. As let-7 is highly conserved among metazoans, our findings will be relevant for mechanistic studies and therapeutic applications in human cancers.

2018-08-20 | GSE101455 | GEO

ISWI_Q4095.Kc

Project description:modENCODE_submission_3031 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: CHIP-chip EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Cell Line Kc167; Antibody ISWI Q4095 (target is ISWI)

2011-03-09 | E-GEOD-27751 | biostudies-arrayexpress

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