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  • Transcription and pre-mRNA alternative splicing are highly regulated processes that play major roles in modulating eukaryotic gene expression. It is increasingly apparent that other pathways of RNA metabolism, including small RNA biogenesis, can regulate these processes. However, a direct link between alternative pre- mRNA splicing and small RNA pathways has remained elusive. Here we show that the small RNA pathway protein Argonaute-2 (Ago-2) regulates alternative pre-mRNA splicing patterns of specific transcripts in the Drosophila nucleus using genome-wide methods in conjunction with RNAi in cell culture and Ago-2 deletion or catalytic site mutations in Drosophila adults. Moreover, we show that nuclear Argonaute-2 binds to specific chromatin sites near gene promoters and negatively regulates the transcription of the Ago-2-associated target genes. These transcriptional target genes are also bound by Polycomb group (PcG) transcriptional repressor proteins and change during development, implying that Ago-2 may regulate Drosophila development. Impor- tantly, both of these activities were independent of the catalytic activity of Ago-2, suggesting new roles for Ago-2 in the nucleus. Finally, we determined the nuclear RNA-binding profile of Ago-2, found it bound to several splicing target transcripts, and identified a G-rich RNA-binding site for Ago-2 that was enriched in these transcripts. These results suggest two new nuclear roles for Ago-2: one in pre-mRNA splicing and one in transcriptional repression. Input chromatin, 2 replicates of Ago2 ChIP-seq
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  • ChIP-seq and mRNA-seq experiments were performed to understand the role of the CLAMP protein in dosage compensation ChIP-seq experiments compared the binding profiles of CLAMP in male and female cells and mRNA-seq data to define the role of CLAMP in regulating genes on the X-chromosome
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  • We report the usage of ChIP-mass spectrometry in identifying proteins and histone modifications involved in Drosophila dosage compensation. We identified a chromatin targeting factor, CG4747, that is involved in recognition of H3K36me3 and robust recruitment of the Drosophila MSL complex to its correct targets on the male X chromosome. ChIP-seq with PAP antibody of Drosophila larvae expressing C-terminally TAP-tagged CG4747.
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  • Accession Number: GSE38293 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-05-29 Summary: modENCODE_submission_3628 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes. These experiments will be conducted in multiple cell types and developmental tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Developmental Stage: Embryo 0-2h; EXPERIMENTAL FACTORS: Developmental Stage Embryo 0-2h; Antibody dORC2 (target is Drosophila ORC2p); read length (read_length) Contact: Name: DCC modENCODE Organization: Ontario Institute for Cancer Research Laboratory: modENCODE DCC Address: MaRS Centre, South Tower, 101 College Street, Suite 800 Toronto Ontario Canada Email: help@modencode.org Phone: 416-673-8579 Organization: GEO Address: USA
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  • Myc is an important oncogene. It is considered as a transcription factor, but the function of Myc in normal or cancer cells have not been fully understood. In addition, Myc plays a role in cell proliferation and differentiation. It is also important for cell identity and stay on chromatin throughout the cell cycle. However, the inheritance of Myc is still a mystery. Here we study the function and inheritance of Myc in D. melanogaster by mapping the binding sites of Myc during interphase and mitosis using ChIP-seq. DNA sample of ChIP for Myc are collected from Kc cells in interphase or mitosis. Input sequences from previous study in the same cell type (GSM762848, GSM762849) are used as control.
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  • Drosophila
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  • Accession Number: GSE25709 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2010-12-04 Summary: ChiP-seq profiling of Drosophila melanogaster salivary glands to identify targets for NSL1 and MCRS2. ArrayExpress Release Date: 2010-04-16 Publication Title: The Nonspecific Lethal Complex Is a Transcriptional Regulator in Drosophila Publication Author List: Raja SJ, Charapitsa I, Conrad T, Vaquerizas JM, Gebhardt P, Holz H, Kadlec J, Fraterman S, Luscombe NM, Akhtar A. Person Roles: submitter Person Last Name: Vaquerizas Person First Name: Juan Person Mid Initials: M Person Email: jvaquerizas@ebi.ac.uk Person Phone: Person Address: Person Affiliation: EBI Overall Design: Experimental Design: individual_genetic_characteristics_design Experimental Design: in_vivo_design Experimental Design: binding_site_identification_design Experimental Design: ChIP-seq Experimental Factor Name: CHIP-ANTIBODY Experimental Factor Type: Chip-antibody Contact: Name: ArrayExpress EBI Organization: European Bioinformatics Institute Laboratory: ArrayExpress Address: Wellcome Trust Genome Campus Hinxton Cambridgeshire United Kingdom Email: miamexpress@ebi.ac.uk Organization: GEO Address: USA
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  • Accession Number: GSE55932 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2014-11-10 Summary: We analyzed gamma-H2Av ChIP-Seq from hand dissected salivary glands of wandering third instar larvae from wild-type (OrR) or suppressor of under-replication (SuUR) mutant Drosophila. Goals were to determine the DNA damage profile relative to underreplicated domains. We analyzed SUUR and Cdc45 ChIP-Seq from hand dissected early (stage 10) and late (stage 12/13) egg chambers from adult Drosophila ovaries. The goals was to determine the localization of SUUR relative to replication forks. Overall Design: ChIP-Seq of gamma-H2Av bound to third instar salivary gland DNA in WT and SuUR mutant Drosophila, analyzed by Illumina sequencing. One replicate is included for each of OrR (WT) or SuUR salivary glands.Rabbit IgG controls are included for OrR (WT). ChIP-Seq of SUUR and Cdc45 bound to egg chamber DNA from early and late stage egg chambers, analyzed by Illumina sequencing. One replicate is included for each ChIP reaction. Contact: Name: Terry L. Orr-Weaver Organization: Whitehead Institute for Biomedical Research Laboratory: Orr-Weaver Address: 9 Cambridge Center Cambridge MA 02142 USA Email: weaver@wi.mit.edu Phone: 617-258-5251 Organization: GEO Address: USA
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  • Accession Number: GSE64464 Platform: GPL14601: AB SOLiD 4 System (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2015-11-06 Summary: CREB-binding protein (CBP, also known as nejire) is a transcriptional co-activator that is conserved in metazoans. We have generated CBP ChIP-seq data from Drosophila S2 cells and compared it to modENCODE data. This shows that CBP is bound at genomic sites with a wide range of functions. As expected, we find that CBP is bound at active promoters and enhancers. In addition, we find that the strongest CBP sites in the genome are found at Polycomb Response Elements embedded in histone H3 lysine 27 trimethylated (H3K27me3) chromatin, where they correlate with binding of the Pho repressive complex. Interestingly, we find that CBP also binds to most insulators in the genome. At a subset of these, CBP may regulate insulating activity, measured as the ability to prevent repressive H3K27 methylation from spreading into adjacent chromatin. Overall Design: ChIP seq in Drosophila S2 cells using two different antibodies against CBP (nejire), one raised in rabbit against amino acids 2540-3190 (CBP rb), and one raised in guinea-pig against amino acids 1-178 (CBP gp) Contact: Name: Mattias Mannervik Organization: Stockholm University Laboratory: Mattias Mannervik Deparment: Molecular Biosciences, the Wenner-Gren Institute Address: Arrheniuslaboratories E3 Stockholm 10691 Sweden Email: mattias.mannervik@su.se Organization: GEO Address: USA
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  • Accession Number: GSE60428 Platform: GPL11203: Illumina Genome Analyzer IIx (Drosophila melanogaster) GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) GPL15872: Illumina Genome Analyzer IIx (Drosophila yakuba) GPL15873: Illumina Genome Analyzer IIx (Drosophila virilis) GPL17484: Illumina Genome Analyzer IIx (Drosophila simulans) GPL17883: Illumina Genome Analyzer IIx (Drosophila pseudoobscura) Organism: Drosophila melanogaster Published on 2014-10-20 Summary: We report the evolutionary behaviour of Polycomb group proteins, their recruitment factors and their underlying sequences by performing ChIP-seq analysis in 4-5 different Drosophila species. We demonstrate an extremely high conservation of Polycomb repressive domains across Drosophila species We validate few cases of PRE divergence that shows that cis-driven PRE evolution is a rare event. We further show that PHO recruitment to Polycomb domains is evolutionarily robust to motif changes and that PRC1 stabilizes binding of its key recruiter Overall Design: ChIP-seq analysis of histone marks and chromatin associated factors across 4-5 Drosophila species Contact: Name: Bernd Schuettengruber Organization: Institute de Génétique Humaine Laboratory: Cavalli Address: 141, rue de la cardonille Montpellier 34396 France Email: bernd.schuttengruber@igh.cnrs.fr Organization: GEO Address: USA
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