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  • In order to idetify paused promoters in vivo, we performed tissue specific Pol II Chip-seq using mutant embryos for the dorsal gradient. We used two population of cells, either dorsal ectoderm cells (gd7 embryos) or mesodermal cells (Toll10b) embryos. ChIP-seq for Pol II in various Drosophila embryos
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  • Mono-methylation of histone H3 on lysine 4 (H3K4me1) and acetylation of histone H3 on lysine 27 (H3K27ac) are histone modifications that are highly enriched over the body of actively transcribed genes and enhancers. Although in yeast all H3K4 methylation patterns including H3K4me1 are implemented by Set1/COMPASS, there are three classes of COMPASS-like complexes in Drosophila that could carry out H3K4me1 on enhancers: dSet1, Trithorax and Trithorax-related (Trr). Here, we report that Trr, the Drosophila homolog of mammalian Mll3/4, can function as a major H3K4 mono-methyltransferase on enhancers in vivo. Loss of Trr results in a global decrease of H3K4me1 and H3K27ac in various tissues. Assays with the cut wing margin enhancer imply a functional role for Trr in enhancer-mediated processes. A genome-wide analysis demonstrates that Trr is required for H3K4me1 and H3K27ac on chromatin signatures that resemble the histone modification patterns described for enhancers. Since Trr and mammalian Mll3/4 complexes are distinguished by bearing a unique subunit, the H3K27 demethylase UTX, we propose a model in which the H3K4 mono-methyltransferase Trr, and the H3K27 demethylase, UTX, cooperate to regulate the transition from inactive/poised to active enhancers. ChIP-seq of Trr, LPT, UTX in Drosophila S2 Cells. ChIP-seq of H3K4me1, H3K4me3, H3K27ac, H3K27me3 in WT and Trr knock-down Drosophila S2 cells. ChIP-seq of H3K4me1, H3K27me3 in LPT knock-down Drosophila S2 cells. ChIP-seq of LPT and UTX in Trr knock-down Drosophila S2 cells. ChIP-seq of H3K4me1 and H3K27me3 in MLL1(+/+), MLL1(-/-), MLL3(+/+), and MLL3(-/-) Mouse Embryonic Fibroblasts (MEFs).
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  • Accession Number: GSE51134 Platform: GPL15334: Illumina HiSeq 1000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2013-09-25 Summary: 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. Overall Design: Input chromatin, 2 replicates of Ago2 ChIP-seq Contact: Name: Matthew Taliaferro Organization: MIT Deparment: Biology Address: 77 Massachusetts Ave Cambridge MA 02144 USA Organization: GEO Address: USA
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  • 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 ChIP-seq analysis of histone marks and chromatin associated factors across 4-5 Drosophila species
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  • Accession Number: GSE27078 Platform: GPL9061: Illumina Genome Analyzer II (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-08-30 Summary: LID is a histone demethylase acting on H3K4me3, a mark related to transcription and found near the transcription start sites (TSS) of the genes. We analyzed where LID is localized and the effects of LID downregulation in the distribution of H3K4me3. Overall Design: Analysis of LID-binding sites in wild type, and of H3K4me3-binding sites in wild type and LID RNAi wing imaginal discs. Contact: Name: David Rossell Organization: IRB Barcelona Address: Baldiri Reixac 10 Barcelona 08028 Spain Email: david.rossell@irbbarcelona.org Organization: GEO Address: USA
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  • 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.
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  • Accession Number: GSE38559 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-06-07 Summary: modENCODE_submission_4352 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: Cell Line: CME-W1-Cl.8+; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Sex: Male; EXPERIMENTAL FACTORS: Antibody Anti-RNA polymerase II clone CTD4H8 (target is RNA polymerase II) 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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  • 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: GSE50819 Platform: GPL11000: Illumina Genome Analyzer (Drosophila yakuba) Organism: Drosophila yakuba Published on 2013-09-13 Summary: This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor H3K27me3 from D.yak_WPP generated by ChIP and analyzed on Illumina Genome Analyzer. Overall Design: A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Factors binding profiles are generated by using specific antibodies for the protein of interest. Contact: Name: Kevin P. White Organization: University of Chicago Deparment: Institute for Genomics and Systems Biology Address: 900 E. 57th STR. 10th FL. Chicago IL 60615 USA Email: kpwhite@uchicago.edu Organization: GEO Address: USA
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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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