Genome-wide identification of PPD2 target genes
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina Genome Analyzer II
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Plant Systems Biology data submission
PROVIDER: E-MTAB-3046 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The Arabidopsis basic leucine zipper transcription factor bZIP29 of the bZIP group I TF family, expressed mainly in proliferative tissues, is functionally characterized in this study. Genes bound by bZIP29 were mapped genome-wide using a tandem ChIP procedure (TChAP) on cell cultures expressing the TF fused to the His-Bio-His tag. The generated data suggests that bZIP29 might be an important player in the reorganization of cell walls during cell proliferation.
2017-05-13 | E-MTAB-3754 | biostudies-arrayexpress
Project description:Genome-wide identification of transcription factor (TF) binding sites is pivotal to our understanding of gene expression regulation. Although much progress has been made in the determination of potential binding regions of proteins by chromatin immunoprecipitation (ChIP), this method has some inherent limitations regarding DNA enrichment efficiency and antibody necessity. Here, we report an alternative strategy for assaying in vivo TF-DNA binding in Arabidopsis thaliana cells by tandem chromatin affinity purification (TChAP). Evaluation of TChAP using the E2Fa TF and comparison with traditional ChIP and single chromatin affinity purification illustrates the suitability of TChAP and provides a resource for exploring the E2Fa transcriptional network. Integration with transcriptome, cis-regulatory element, functional enrichment, and co-expression network analyses demonstrates the quality of the E2Fa TChAP-seq data and validates the identification of new direct E2Fa targets. TChAP enhances both TF target mapping throughput, by circumventing issues related to antibody availability, and output, by improving DNA enrichment efficiency. Illumina Seq analysis of E2Fa bound DNA elements isolated using different chromatin isolation methods. BioProject PRJNA172013; SRA study ID SRP014713
2014-02-04 | E-GEOD-53422 | biostudies-arrayexpress
Project description:To identify the genomic binding sites of FRS12, Tandem Chromatin Affinity Purification â Seq (TChAP-Seq) was performed on 7-d-old Pro35S:FRS12-HBH and Pro35S:NLS-GFP-HBH expressing Arabidopsis thaliana PSB-D cells. Cultures were transferred to long days (16:8) conditions two weeks before harvesting at night time (NT) at zeitgeber time (ZT) 20 (time of lights on usually defines zeitgeber time zero). Chromatin was isolated from formaldehyde-treated cell cultures following two affinity purification steps; first by IMAC using a Ni-NTA Superflow resin (Qiagen), then by a Biotin binding step using a Streptavidin Sepharose resin (GE Healthcare). Finally, protein-DNA bound fragments were decrosslinked, deproteinized and purified using QIAquick PCR Purification Kit (Qiagen). Pro35S:FRS12-HBH samples were carried in two replicates whereas background Pro35S:NLS-GFP-HBH sample was prepared in a single replicate. The TChAP DNA samples were processed by first preparing a TruSeq ChIPseq library (Illumina) and then sequenced using Illumina HiSeq 2000 at 50bp single read at an average depth of 15 million reads.
2017-02-04 | E-MTAB-3019 | biostudies-arrayexpress
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
Project description:Background : Candida albicans is a diploid pathogenic fungus not yet amenable to routine genetic investigations. Understanding aspects of the regulation of its biological functions and the assembly of its protein complexes would lead to further insight into the biology of this common disease-causing microbial agent. Results: We have developed a toolbox allowing in vivo protein tagging by PCR-mediated homologous recombination with TAP, HA and MYC tags. The transformation cassettes were designed to accommodate a common set of integration primers. The tagged proteins can be used to perform tandem affinity purification (TAP) or chromatin immunoprecipitation coupled with microarray analysis (ChIP-CHIP). Tandem affinity purification of C. albicans Nop1 revealed the high conservation of the small processome composition in yeasts. Data obtained with in vivo TAP-tagged Tbf1, Cbf1 and Mcm1 recapitulates previously published genome-wide location profiling by ChIP-CHIP. We also designed a new reporter system for in vivo analysis of transcriptional activity of gene loci in C. albicans. Conclusion: This toolbox provides a basic setup to perform purification of protein complexes and increase the number of annotated transcriptional regulators and genetic circuits in C. albicans.
2008-11-15 | GSE13427 | GEO
Project description:Background : Candida albicans is a diploid pathogenic fungus not yet amenable to routine genetic investigations. Understanding aspects of the regulation of its biological functions and the assembly of its protein complexes would lead to further insight into the biology of this common disease-causing microbial agent. Results: We have developed a toolbox allowing in vivo protein tagging by PCR-mediated homologous recombination with TAP, HA and MYC tags. The transformation cassettes were designed to accommodate a common set of integration primers. The tagged proteins can be used to perform tandem affinity purification (TAP) or chromatin immunoprecipitation coupled with microarray analysis (ChIP-CHIP). Tandem affinity purification of C. albicans Nop1 revealed the high conservation of the small processome composition in yeasts. Data obtained with in vivo TAP-tagged Tbf1, Cbf1 and Mcm1 recapitulates previously published genome-wide location profiling by ChIP-CHIP. We also designed a new reporter system for in vivo analysis of transcriptional activity of gene loci in C. albicans. Conclusion: This toolbox provides a basic setup to perform purification of protein complexes and increase the number of annotated transcriptional regulators and genetic circuits in C. albicans. Two independent biological replicates of ChIP-CHIP of Mcm1-TAP in yeast and hyphal states. ChIP-CHIP of Cbf1-TAP and Tbf1-TAP.
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Project description:A PSB-D wild type Arabidopsis thaliana cell culture (Arabidopsis Biological Resource Center stock: CCL84840) was grown after subculturing for one week and divided into separate 10 mL samples for 24 h. Samples were then treated with 50 µM RubNeddin1 (RN1, Chembridge ID 6389186), 2,4-D, or an equal volume of DMSO. Total RNA was extracted from each 10 mL cell culture sample, for each of at least 3 biological replicates, RQ1 RNase-free DNase (Promega) was used for the on-column DNase digestion step. A Trueseq RNA-Seq library (Illumina) was compiled and sequenced as 50-bp single read using Illumina HiSeq 2000. Control samples (3) for this experiment were submitted under accession number E-MTAB-3915
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Project description:We used ChIP-chip to map the binding of C-terminally TAP (tandem affinity purification)-tagged GalR (tagged at its native locus in an unmarked strain) across the E. coli genome.
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Project description:The quiescent center (QC) plays an essential role during root development by creating a microenvironment that preserves the stem cell fate of its surrounding cells. Strikingly, in order to retain root structure, QC cells only occasionally self-renew, displaying a proliferation rate far below that of all other cells within the root meristem. Previously, the APC/CCCS52A2 ubiquitine ligase and brassinosteroid signaling pathways have been found to antagonistically control Arabidopsis thaliana QC cell proliferation. Here, we demonstrate that both pathways converge on the ERF115 transcription factor that acts as a rate-limiting factor of QC cell division through transcriptional control of the autocrine phytosulfokine PSK5 peptide hormone. ERF115 marks QC cell division but is restrained through proteolysis by the APC/CCCS52A2 ubiquitine ligase, whereas QC proliferation is driven by brassinosteroid-dependent ERF115 expression. Combined, these two antagonistic mechanisms delimit the ERF115-PSK5 activity and QC renewal. Our results reveal a unique cell cycle regulatory mechanism that accounts for the low proliferation rate of QC cells within a surrounding population of highly mitotic active cells. ChIP-seq analysis of genes bound by the ERF115 transcription factor, using mock ChIP with wild type cells as negative control. Analyzed by Illumina HiSeq
2013-11-04 | E-GEOD-48793 | biostudies-arrayexpress