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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Drosophila ROW RNAi gene expression profiling

ABSTRACT: Heterochromatin-protein 1 (HP1) is a functionally diverse family of proteins. In particular, Drosophila dHP1c forms a complex with the transcription factors WOC and ROW (dHP1EU) that localizes at euchromatin and regulates gene expression. We used microarrays to analyse the changes in gene expression after row depletion by RNAi. For expression profiling analyses, total RNAs were prepared from control S2 cells and upon RNAi-mediated depletion of ROW, converted to cDNA and hybridized to Drosophila Genome 2.0 GeneChip (Affymetrix).

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Oscar Reina Garcia

PROVIDER: E-GEOD-49103 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Drosophila ROW RNAi gene expression profiling

Project description:Heterochromatin-protein 1 (HP1) is a functionally diverse family of proteins. In particular, Drosophila dHP1c forms a complex with the transcription factors WOC and ROW (dHP1EU) that localizes at euchromatin and regulates gene expression. We used microarrays to analyse the changes in gene expression after row depletion by RNAi.

2015-05-01 | GSE49103 | GEO

dDsk2 stabilizes dHP1c binding at TSS [ChIP-Seq]

Project description:The Drosophila ubiquitin receptor dDsk2 associates to chromatin and stabilizes binding of the euchromatic dHP1c/WOC/ROW-complex (dHP1EU) to the transcription-start site (TSS) of active genes ChIP-Seq peak calling of WOC, ROW, Z4, HP1c and Dsk2 against Input sample in Drosophila melanogaster S2 cells

2015-05-01 | E-GEOD-49102 | biostudies-arrayexpress

The Genomic Binding Profile of GAGA Element Associated Factor (GAF) in Drosophila S2 cells

Project description:GAGA associated transcription factor (GAF) is a highly abundant and essential protein in Drosophila. GAF recognizes and binds arrays of GA dinucleotides via a zinc finger DNA binding domain to regulate transcription by binding to general TF machinery or recruit nucleosome remodeling factors. We performed GAF ChIP-seq to quantify the intensity of GAF binding at high resolution in S2 cells. In addition, we performed GAF ChIP-seq in S2 cells that were depleted of GAF by RNAi. By quantifying the degree to which all GAF binding sites are susceptible to GAF depletion, we found the cellular degree of depletion does not translate equally to the depletion of GAF at individual chromatin bound sites. For example, some high intensity GAF binding sites were completely unaffected by GAF depletion, while lower affinity binding sites were often ablated upon GAF depletion. These data sets will serve as a valuable resource to others who study the dynamic interplay between GAF and chromatin. We also compared the GAF binding sites to the full set of genomic ChIP data that is available for S2 cells and compared the intensity for each factor and histone modification/variant. Lastly, we investigated the influence that GAF had upon inducible transcription factor binding using the heat shock system. A single mock immunoprecipitation (IP) using non-specific IgG was used as a background dataset for this study (see PMID: 20844575; GSM470838). We performed two independent GAF-ChIP-seq experiments in untreated S2 cells and two replicates in S2 cells that were depleted of GAF by RNAi.

2013-08-01 | E-GEOD-40646 | biostudies-arrayexpress

RNA-seq of D. melanogaster S2 cells upon depletion of dCoREST and its interacting partners compared to control

Project description:RNAi KD of dCoREST, dLSD1, dL(3)mbt, dLint-1, dG9a and EGFP (control) followed by determination of gene transcription changes by RNA-seq

2019-01-01 | E-MTAB-7440 | biostudies-arrayexpress

CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy [MNase-seq]

Project description:MNase-seq was performed in order to analyze changes in nucleosomal occupancy after depletion of CTCF/P190 and ISWI from Drosophila S2 cells MNase-seq from Drosophila S2 nuclei after CTCF/CP190 or ISWI-specific RNAi treatment

2014-08-11 | E-GEOD-51599 | biostudies-arrayexpress

Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [Beaf-32 ChIP-seq]

Project description:Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify ‘indirect peaks’ of multiple IBPs, that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common co-factors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions. Binding profiles of Beaf-32 in Drosophila S2 cells by ChIP-Seq (Illumina)

2014-02-01 | E-GEOD-52962 | biostudies-arrayexpress

Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [CP190 ChIP-Seq]

Project description:Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify ‘indirect peaks’ of multiple IBPs, that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common co-factors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions. Binding profiles of CP190 in stably transfected Drosophila S2 cell lines expressing in Wild-Type Beaf (Control) or Mutant Beaf by ChIP-Seq (Illumina)

2014-02-01 | E-GEOD-52886 | biostudies-arrayexpress

CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy [ChIP-seq]

Project description:H3-ChIP-seq was performed in order to analyze changes in nucleosomal occupancy after depletion of CTCF/P190 and ISWI from Drosophila S2 cells Histone H3 ChIP-seq from Drosophila S2 cells after CTCF/CP190 or ISWI-specific RNAi treatment

2014-08-11 | E-GEOD-51598 | biostudies-arrayexpress

The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes [RNA_seq_S2]

Project description:Chromatin insulators are involved in transcription regulation and long-range chromatin contacts. In Drosophila the Boundary Element-Associated Factor Of 32kD (BEAF-32) binds to promoters of housekeeping genes and the boundaries of Topological Associated Domains (TAD) and is involved in the regulation of long-range targets by mechanisms that remain incompletely understood. Here we show that Relative-Of-WOC (ROW), which is part of the Heterochromatin Protein 1c (HP1c) complex, is essential for the long-range transcription regulation mediated by BEAF-32. We found that ROW physically interacts with the insulator complex proteins BEAF-32 and Chromator, as well as with HP1c, HP1b, and Without Children (WOC). Moreover, we found that ROW binds AT-rich sequences flanked by BEAF-32 motifs, which are located at promoters of housekeeping genes and in TAD boundaries. In agreement with these results, the genome distribution of ROW strongly correlated with BEAF-32 and WOC, but at a lower level with HP1c and HP1b. Knockdown of row resulted in downregulation of genes that are long-range targets of BEAF-32, are indirectly bound by BEAF-32 and ROW, and enriched with factors associated with RNA polymerase II pausing. These results suggest that ROW and BEAF-32 are involved in the recruitment of protein complexes required for transcription activation and long-range contacts between promoters of housekeeping and inducible genes.

2022-07-14 | GSE169413 | GEO

The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes [RNA_seq_flyheads]

2022-07-14 | GSE169412 | GEO

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