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Generation of chromatin maps for ASH1 and FSH applying ChIP-seq

ABSTRACT: see Super Series Summary Cross-linked chromatin derived from Drosophila S2-DRSC cells was immunoprecipitated using antibodies targeting ASH1 and FSH. Precipitated chromatin was sequenced applying Illumina sequencing.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Tobias Kockmann

PROVIDER: E-GEOD-36404 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila

Project description:Background: The question of how cells re-establish gene expression states after cell division is still poorly understood. Genetic and molecular analyses have indicated that Trithorax group (TrxG) proteins are critical for the long-term maintenance of active gene expression states in many organisms. A generally accepted model suggests that TrxG proteins contribute to maintenance of transcription by protecting genes from inappropriate Polycomb group (PcG)-mediated silencing, instead of directly promoting transcription. Results: Here we report a physical and functional interaction in Drosophila between two members of the TrxG, the histone methyltransferase ASH1 and the bromodomain and extraterminal family protein FSH. We investigated this interface at the genome level, uncovering a widespread colocalization of both proteins at promoters and PcG-bound intergenic elements. Our integrative analysis of chromatin maps and gene expression profiles revealed that the observed ASH1-FSH binding pattern at promoters is a hallmark of active genes. Inhibition of FSH-binding to chromatin resulted in global down-regulation of transcription. In addition, we found that genes displaying marks of robust PcG-mediated repression also have ASH1 and FSH bound to their promoters. Conclusions: Our data strongly favor a global coactivator function of ASH1 and FSH during transcription, as opposed to the notion that TrxG proteins impede inappropriate PcG-mediated silencing, but are dispensable elsewhere. Instead, our results suggest that PcG repression needs to overcome the transcription-promoting function of ASH1 and FSH in order to silence genes. Refer to individual Series

2013-02-06 | E-GEOD-36450 | biostudies-arrayexpress

Chromatin maps of the Drosophila melanogaster TrxG protein Ash1 and FSH

Project description:Trithorax group (TrxG) proteins counteract Polycomb silencing by an as yet uncharacterized mechanism. A well-known member of the TrxG is the histone methyltransferase Absent, Small, or Homeotic discs 1 (ASH1). In Drosophila ASH1 is needed for the maintenance of Hox gene expression throughout development, which is tightly coupled to preservation of cell identity. In order to understand the molecular function of ASH1 in this process, we performed affinity purification of tandem-tagged ASH1 followed by mass spectrometry (AP-MS) and identified FSH, another member of the TrxG as interaction partner. Here we provide genome-wide chromatin maps of both proteins based on ChIP-seq. Our Dataset comprises of 4 ChIP-seq samples using chromatin from S2 cells which was immunoprecipitated, using antibodies against Ash1, FSH-L and FSH-SL.

2013-06-30 | E-GEOD-30820 | biostudies-arrayexpress

Regulation of Megakaryocytic differentiation in Cell Line Models by Dynamic Combinatorial Interactions of RUNX1 with Its Cooperating Partners

Project description:Regulation of Megakaryocytic differentiation in Cell Line Models by Dynamic Combinatorial Interactions of RUNX1 with Its Cooperating Partners Examination of RUNX1 binding in K562 cells, before and following TPA induction and CMK cells. Examination of GATA1 and FOS binding and H3K4me1 and H3K27me3 modification levels following TPA induction in K562 cells.

2011-01-10 | E-GEOD-24777 | biostudies-arrayexpress

Dynamic combinatorial interactions of RUNX1 and cooperating partners regulates megakaryocytic differentiation in cell line models

Project description:This SuperSeries is composed of the following subset Series: GSE24777: Regulation of Megakaryocytic differentiation in Cell Line Models by Dynamic Combinatorial Interactions of RUNX1 with Its Cooperating Partners GSE24778: Expresssion data in K562 cells, before and after TPA induction and including a RUNX1 knockout construct or a control structure Refer to individual Series

2011-01-10 | E-GEOD-24779 | biostudies-arrayexpress

Genome-wide profiling of H3K27ac (ChIP-seq) in IMR90 cells

Project description:To determine the genome-wide pattern of H3K27ac in IMR90 (ATCC CCL-186) cells we performed ChIP-seq upon hormone treatment (1.5 h, 1 M dexamethasone).

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Addiction of t(8;21) and inv(16) AML to native RUNX1 [ChIP-Seq data]

Project description:Cancer cells maintain a sensitive balance between growth-promoting oncogenes and apoptosis inhibitors. We show that WT RUNX1 is required for survival of t(8;21)-Kasumi-1 and inv(16)-ME-1 AML cell lines. The malignant AML phenotype is sustained by a delicate AML1-ETO/RUNX1 balance that involves competition for common DNA binding sites regulating a subset of AML1-ETO/RUNX1 targets. Genomewide sequencing data is included herein: Transcription factors RUNX1 c-terminus and n-terminus which is shared with AML1-ETO were profiled independently), AML1-ETO and AP4 were profiled using ChIP-Seq in Kasumi-1 cells, as well as control ChIP-Seq experiments of non immune serum. Two replicates were performed for each transcription factor profiling and control experiment.

2013-08-18 | E-GEOD-45738 | biostudies-arrayexpress

Identification of novel immunodominant proteins from Campylobacter jejuni and the characterization of linear epitopes

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-04-06 | E-GEOD-44717 | biostudies-arrayexpress

Verification of immunogenic nature by microarray screening

Project description:Screening of 22 novel proteins derived from Campylobacter jejuni NCTC 11168 identified prior via screening of cDNA libraries. The full-length proteins were attached using a specific HaloTag to their corresponding ligand surface, HaloLink. Screening was performed using three different polyclonal antibodies to Campylobacter jejuni and detection was achieved by goat polyclonal antibody to rabbit IgG conjugated with Chromeo-546. In order to assess their potential immungenic nature and rank the proteins investigated, comparative analysis using already described antigens from C. jejuni were used in the assay. Each microarray was separated into different incubation chambers using the ProPlate (Grace Biolabs) multi-well gaskets. While for two slides (2009 and 2447), three chambers were used, the remaining slides were designed to use 16 different compartments. Each compartment could be incubated with different antibodies and represent individual replicates of the slides. As positive references, hisJ and cjaA were used. For negative controls, argC and gapA were used, and the crude lysates of the expression host (Acella E. coli) and buffer were spotted as well. For slides 2009 and 2447, three-well gaskets were used allowing for seven replicates per sample, while only incubation with one antibody. Slides 416033 and 416826 used 16-well gaskets and only hisJ and argC as protein references. Samples and controls were spotted in quadruplicate. Finally, for 1000 and 1001, samples were spotted in triplicate, whereas controls were spotted in quadruplicate using hisJ, cjaA, argC and gapA as protein references.

2013-04-06 | E-GEOD-45520 | biostudies-arrayexpress

ChIP-seq of E4F1 in primary mouse embryonic fibroblasts (MEFs) and in p53-/-, Ha-RasV12-transformed MEFs

Project description:E4F1 is a ubiquitously expressed zinc-finger protein of the Gli-Kruppel family that was first identified, more than 30 years ago, as a cellular target of the adenoviral oncoprotein E1A13S (Ad type V), required for transcriptional regulation of adenoviral genes. In order to decipher E4F1 cellular target genes, we performed chromatin immunoprecipitation of endogenous E4F1 in primary and in p53KO, Ha-RasV12-transformed MEFs. Both input and immunoprecipitated DNA were exhaustively sequenced and mapped on the mouse genome (mm9). Peak detection has been achieved by combining two peak calling algorithms. Intersection of the two E4F1 peak lists on each cell line were considered as E4F1 chromatin bound regions. Genome-wide mapping of E4F1 binding in mouse embryonic fibroblasts.

2015-04-01 | E-GEOD-57228 | biostudies-arrayexpress

Epitope mapping of potential novel immunogenic proteins of Campylobacter jejuni NCTC 11168

Project description:A number of seven proteins were selected during immunoscreening and further analyses. The proteins were in silico divided into overlapping 15-mer oligopeptides with an overlap of 11 residues. The microarrays were incubated with different antibodies to C. jejuni, Escherichia coli and Salmonella enterica. Each microarray was separated into three individual incubation chambers using ProPlate 3-Well modules. Within each incubation chamber, each peptide was spotted in triplicate with the controls spotted nine times each. The controls included human-IgG, rabbit-IgG, mouse-IgG and myelin basal protein (MBP). Each chamber was incubated independently using different polyclonal antibodies to C. jejuni, and for specificity testing, with an antibody to E. coli or S. enterica. Thus, samples 4_1, 4_2, 5_1 and 5_2 represent epitope mapping of three proteins with C. jejuni antibodies, while 6_1, 6_2, 7_1 and 7_2 represent the data after incubation with an E. coli antibody investigating unspecific interactions of the antibody to the potential linear epitopes from C. jejuni. Finally, for four different proteins from C. jejuni, the set two indicated by S2 was performed. Here, S2_6_1, S2_7_1, S2_7_2, S2_8_1 and S2_8_2 indicate epitope mapping after incubation with antibodies to C. jejuni, while the remaining samples were performed to test these latter 4 proteins for specificity by incubation with antibody to S. enterica.

2013-04-06 | E-GEOD-45542 | biostudies-arrayexpress

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