Project description:We have investigated the effect of RRP6 depletion on the transcriptome of S2 cells using Illumina deep RNA sequencing. We have also carried out Illumina ChIP-seq analysis of RRP6 genome occupancy in control S2 cells (GFP-KD) and in cells depleted of SU(VAR)3-9.
Project description:We have investigated the effect of RRP6 depletion on the transcriptome of S2 cells using Affymetrix whole-genome tiling arrays. We have also carried out Illumina ChIP-seq analysis of RRP6 genome occupancy in control S2 cells (GFP-KD) and in cells depleted of SU(VAR)3-9.
Project description:We have carried out ChIP-seq to study the distribution of Brahma in the genome of S2 cells and to identify the Brahma-bound genes. We have also knocked down Brahma by RNA interference and we have carried out RNA-seq to determine the changes induced by Brahma depletion in the transcriptome of S2 cells. Furthermore, we have carried out RNA-seq experiments to profile S2 cells in which we first deplete Brahma by RNA interference and then express recombinant Brahma (either wild-type or ATPase mutant). These datasets are being used in several projects aimed at gaining understanding on the roles of Brahma in transcription regulation and pre-mRNA processing.
Project description:The liver-specific microRNA, miR-122, is an essential host factor for replication of hepatitis C virus (HCV), an important infectious cause of chronic liver disease and hepatocellular carcinoma. miR-122 stabilizes the positive-strand HCV RNA genome and promotes viral RNA synthesis by binding two closely spaced sites (S1 and S2) near the 5’ end of the genome in association with Ago2. Ago2 is essential for both host factor activities, but whether other host proteins are involved is unknown. Using a quantitative proteomics approach, we identified TNRC6A (GW182) and its paralogs (TNRC6B and TNRC6C), as functionally important components of the miR-122/Ago2 host factor complex binding HCV RNA. Depletion of any two TNRC6 proteins reduced HCV replication in Huh-7.5 cells,but did not reduce viral RNA stability or translational activity, but rather dampened miR-122 stimulation of viral RNA synthesis. However, TNRC6 depletion had no effect on replication of HCV in which S2 was mutated so that miR-122 binds only S1, whereas it significantly enhanced replication when S1 was mutated and only S2 bound by miR-122. Consistent with this, we found that TNRC6 proteins preferentially associate with the S1 site, and that the association of Ago2 with S2 is increased in TNRC6-depleted cells. Collectively, these data suggest a model in which TNRC6 proteins, which are known to interact with Ago2, preferentially direct the miR-122/Ago2 complex to S1 while restricting its association with S2, thereby fine tuning the spatial organization of miR-122/Ago2 complexes bound to the viral RNA.
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. 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).
Project description:The exosome complex and its' subunits are vital for proccessing and or degrading many cellular RNAs. We used microarrays to detail the global changes in mRNA levels in response to exosome subunit depletion. RNA was extracted from dsRNA treated S2 cells and hybridized using Affymetrix microarrays. We aimed to obtain a master set of mRNAs surveyed by exosme subunits in vivo.
Project description:RNAi of signal transduction components in Drosophila S2 cells We performed RNAi knockdown experiments on 15 different signal transduction components in Drosophila S2 cells and prepared RNA libraries from the poly-adenylated fraction of the RNA. SOLiD sequencing of strand-specific, barcoded transcriptome libraries yielded expression profiles allowing us to extract common pathway signatures and indicated that Cka may function as novel regulator in Ras/MAPK signaling. ArrayExpress Release Date: 2011-07-08 Person Roles: investigator Person Last Name: Boutros Person First Name: Michael Person Email: m.boutros@dkfz.de Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany Person Affiliation: Signaling and Functional Genomics, DKFZ Person Roles: investigator Person Last Name: Sandmann Person First Name: Thomas Person Email: t.sandmann@dkfz.de Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany Person Affiliation: Signaling and Functional Genomics, DKFZ Person Roles: investigator Person Last Name: Horn Person First Name: Thomas Person Email: t.horn@dkfz.de Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany Person Affiliation: Signaling and Functional Genomics, DKFZ Person Roles: submitter Person Last Name: Kerr Person First Name: Grainne Person Email: g.kerr@dkfz.de Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany Person Affiliation: Signaling and Functional Genomics, DKFZ
Project description:We analyzed transcriptional effects after depletion of Drosophila melanogaster S2 cells from CTCF via specific dsRNA treatment in comparison to cells treated with control dsRNA.
Project description:We analyzed transcriptional effects after depletion of Drosophila melanogaster S2 cells from CP190 via specific dsRNA treatment in comparison to cells treated with control dsRNA.