Dorsal dependent CBP binding on a genome wide scale
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE34221 | GEO | 2012/06/29
SECONDARY ACCESSION(S): PRJNA149815
REPOSITORIES: GEO
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Project description:We find a high concordance between the binding of the Drosophila transcription factor Dorsal and the co-activator CBP during early embryogenesis. This relationship was furter examined by comparing CBP distribution in Drosophila embryos derived from wt and mutant flies lacking intranuclear Dorsal (gd7). Our data suggests a specific involvemet of CBP in initiating early dorsoventral patterning, but not in anterioposterior. CBP ChIP seq of 2-4 hours old Drosophila embryos derived from w1118 (wild-type) or gd7 homozygous mutant mothers
2012-06-28 | E-GEOD-34221 | biostudies-arrayexpress
Project description:Genetic studies have identified numerous sequence-specific transcription factors that control development, yet little is known about their in vivo distribution across animal genomes. We determine the genome-wide occupancy of the dorsoventral determinants Dorsal, Twist and Snail in the Drosophila embryo using ChIP-chip analysis. There is a tight correlation between the limits of known enhancers and the in vivo binding of these proteins. The analysis predicts substantially more target genes than previously estimated, including Dpp signaling components and genes encoding anteroposterior segmentation determinants. Thus, the ChIP-chip data uncovers a much larger network, which integrates diverse patterning processes during development.
2007-08-31 | E-TABM-226 | biostudies-arrayexpress
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-chip data on Agilent 244K dual-color arrays for antibody: CBP/p300 at 12 different time-points of Drosophila development. Current Dataset: [GSM386269..GSM386277]: ChIP-chip of CBP in Drosophila embryos at 4-8 hours of development [GSM386279..GSM386287]: ChIP-chip of CBP in Drosophila embryos at 20-24 hours of development [GSM418309..GSM418317]: ChIP-chip of CBP in adult female Drosophila [GSM418318..GSM418326]: ChIP-chip of CBP in adult male Drosophila [GSM418335..GSM418343]: ChIP-chip of CBP in Drosophila embryos at 16-20 hours of development [GSM418454..GSM418462]: ChIP-chip of CBP in Drosophila L3 larvae [GSM418463..GSM418471]: ChIP-chip of CBP in Drosophila pupae [GSM442425..GSM442433]: ChIP-chip of CBP in Drosophila embryos at 0-4 hours of development [GSM443119..GSM443127]: ChIP-chip of CBP in Drosophila L1 larvae For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2009-03-28 | GSE15427 | GEO
Project description: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. 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)
2015-11-06 | E-GEOD-64464 | biostudies-arrayexpress
Project description:Whole-Genome Analysis of Dorsal-Ventral Patterning in the Drosophila Embryo. The maternal Dorsal regulatory gradient initiates the differentiation of several tissues in the early Drosophila embryo. Whole-genome microarray assays identified as many as 40 new Dorsal target genes, which encode a broad spectrum of cell signaling proteins and transcription factors. Evidence is presented that a tissue-specific form of the NF-Y transcription complex is essential for the activation of gene expression in the mesoderm. Tissue-specific enhancers were identified for new Dorsal target genes, and bioinformatics methods identified conserved cis-regulatory elements for coordinately regulated genes that respond to similar thresholds of the Dorsal gradient. The new Dorsal target genes and enhancers represent one of the most extensive gene networks known for any developmental process. Stathopoulos et al., Cell, Vol 111, 687-701, November 2002. Keywords: repeat sample
2002-11-27 | GSE86 | GEO
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-chip data on Agilent 244K dual-color arrays for antibody: CBP/p300 at 12 different time-points of Drosophila development. Current Dataset: [GSM386269..GSM386277]: ChIP-chip of CBP in Drosophila embryos at 4-8 hours of development [GSM386279..GSM386287]: ChIP-chip of CBP in Drosophila embryos at 20-24 hours of development [GSM418309..GSM418317]: ChIP-chip of CBP in adult female Drosophila [GSM418318..GSM418326]: ChIP-chip of CBP in adult male Drosophila [GSM418335..GSM418343]: ChIP-chip of CBP in Drosophila embryos at 16-20 hours of development [GSM418454..GSM418462]: ChIP-chip of CBP in Drosophila L3 larvae [GSM418463..GSM418471]: ChIP-chip of CBP in Drosophila pupae [GSM442425..GSM442433]: ChIP-chip of CBP in Drosophila embryos at 0-4 hours of development [GSM443119..GSM443127]: ChIP-chip of CBP in Drosophila L1 larvae For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays.
2010-06-21 | E-GEOD-15427 | biostudies-arrayexpress
Project description:Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is not fully understood. Here we identify a novel activity of the co-regulator and histone acetyltransferase p300/CBP in positioning promoter-proximal paused Pol II. We find that CBP inhibition impedes transcription through the +1 nucleosome, causing âdribblingâ of Pol II from the canonical pause site genome-wide. We further discovered that promoters strongly occupied by Drosophila CBP and GAGA-factor have high levels of paused Pol II, a unique chromatin signature and strong expression regardless of cell type. Interestingly, CBP activity is rate-limiting for Pol II recruitment to these highly-paused promoters but for transit into elongation at other genes. Thus, we uncover a key role for CBP during transcription in directly controlling different rate-limiting steps depending on promoter features. Examination of transcriptional regulation with and without CBP inhibition for 10 minutes in Drosophila S2 cells. Two biological replicates for each condition.
2016-08-01 | E-GEOD-81649 | biostudies-arrayexpress
Project description:Whole-Genome Analysis of Dorsal-Ventral Patterning in the Drosophila Embryo. The maternal Dorsal regulatory gradient initiates the differentiation of several tissues in the early Drosophila embryo. Whole-genome microarray assays identified as many as 40 new Dorsal target genes, which encode a broad spectrum of cell signaling proteins and transcription factors. Evidence is presented that a tissue-specific form of the NF-Y transcription complex is essential for the activation of gene expression in the mesoderm. Tissue-specific enhancers were identified for new Dorsal target genes, and bioinformatics methods identified conserved cis-regulatory elements for coordinately regulated genes that respond to similar thresholds of the Dorsal gradient. The new Dorsal target genes and enhancers represent one of the most extensive gene networks known for any developmental process. Stathopoulos et al., Cell, Vol 111, 687-701, November 2002.
2008-06-20 | E-GEOD-86 | biostudies-arrayexpress
Project description:A comparative RNA-SEQ analysis of control total RNA preparations from pooled E14.5 dorsal root ganglia was carried out to determine the performance of the RNAseq reactions at differing concentrations (3ng, 10ng & 30ng in high or low volumes) and concordance among different institutions using the same source of RNA. RNA was extracted from E14.5 dorsal root ganglia dissected from wild type C57BL/6J embryos and sequenced using Illumina Hiseq 2500 platform.
2014-12-15 | E-GEOD-63143 | biostudies-arrayexpress
Project description: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.
2015-11-06 | GSE64464 | GEO