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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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ChIP with anti-H3K27me3 to compare binding in salivary glands of WT and SuUR Drosophila

ABSTRACT: ChIP was performed to identify regions of gDNA bound by H3K27me3 in third instar salivary glands of Drosophila WT and SuUR mutants. This demonstrated that H3K27me3 binds differently in under-replicated in SuUR mutant third instar salivary glands. Comparison of H3K27me3 ChIP sample relative to input DNA or control IgG pulldown for two different Drosophila strains

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Terry Orr-Weaver

PROVIDER: E-GEOD-31897 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Developmental Control of Gene Copy Number by Repression of Replication Initiation and Fork Progression

Project description:This SuperSeries is composed of the following subset Series: GSE31895: ChIP with anti-orc2 antibody to identify regions of orc binding in third instar salivary glands of WT and SuUR mutant Drosophila GSE31896: RNAPolII ChIP to find differences between third instar salivary glands of WT and SuUR GSE31897: ChIP with anti-H3K27me3 to compare binding in salivary glands of WT and SuUR Drosophila GSE31898: CGH to ascertain levels of gDNA in third instar salivary glands of various mutant Drosophila GSE31899: ChIP-Seq of ORC2 bound to third instar salivary gland DNA in WT and mutant Drosophila, analyzed by Illumina sequencing GSE33017: Expression profile of third instar larval salivary gland tissue Refer to individual Series

2011-10-17 | E-GEOD-31900 | biostudies-arrayexpress

RNAPolII ChIP to find differences between third instar salivary glands of WT and SuUR

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2011-10-17 | E-GEOD-31896 | biostudies-arrayexpress

ChIP with anti-orc2 antibody to identify regions of orc binding in third instar salivary glands of WT and SuUR mutant Drosophila

Project description:ChIP was performed to identify regions of gDNA bound by orc2 in third instar salivary glands of Drosophila WT and SuUR mutants. This demonstrated that ORC does not localize to regions that are under-replicated in SuUR mutant third instar salivary glands. Comparison of ORC2 ChIP sample relative to input DNA or control IgG pulldown for two different Drosophila strains

2011-10-17 | E-GEOD-31895 | biostudies-arrayexpress

CGH to ascertain levels of gDNA in third instar salivary glands of various mutant Drosophila

Project description:Comparative genomic hybridization was performed to compare levels of gDNA in third instar salivary glands of Drosophila mutants/nulls in the SuUR and orc proteins, compared with 0-2hr diploid embryo gDNA. This illustrates regions of differential replication in the genome. CGH of salivary gland DNA compared with diploid early embryonic samples for four different Drosophila strains

2011-10-17 | E-GEOD-31898 | biostudies-arrayexpress

ChIP-Seq of ORC2 bound to third instar salivary gland DNA in WT and mutant Drosophila, analyzed by Illumina sequencing

Project description:We analyzed ORC2 ChIP-Seq from hand dissected salivary glands of wandering third instar larvae from OrR or SuUR Drosophila. Goals were to ascertain the difference in binding profile between salivary glands expressing and not expressing the Supressor of UnderReplication protein. One replicate is included for each of OrR (WT) or SuUR salivary glands.

2011-10-18 | E-GEOD-31899 | biostudies-arrayexpress

DamID data for SUUR binding in 12-14h Embryo, larval salivary glands and larval brain

Project description:SUUR protein was found to be a major component of three repressive chromatin states named BLACK, BLUE and GREEN chromatins. Here we addressed a question of developmental dynamics of these chromatin states using SUUR as a marker. SUUR binding in larval salivary glands, brains and 12-14 hours embryos was determined using DamID technique. Comparison of Dam-SUUR binding to Dam-alone signal in duplicate for each sample type.

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Examination of H3K27me3 histone modification in 3 cell types in presence or absence of SuUR mutation

Project description:Heterochromatin contains repressively modified histones and replicates late in S phase of the cell cycle. Besides the shortage in replication origins, little is known about replication timing regulation in silenced regions. In Drosophila polytene cells, late replication results in under-replication and decreased DNA copy number in heterochromatic regions of the genome. The Suppressor of Under-replication (SUUR) protein controls this feature â in its absence the DNA polytenization level in most silenced regions is restored, however the repressive histone marks are lost. We hypothesized that SUUR regulates the re-establishment of repressive histone pattern during replication which results in delayed replication completion of heterochromatin. Measuring DNA copy number in mutants with disrupted repressive pathways, we found that under-replication is directly linked to repressive histone marks supply. DamID-seq and ChIP-seq experiments revealed that SuUR mutation does not affect the establishment of heterochromatin domains. Here, we identified a novel SUUR protein interaction (CG12018) that supports SUUR association with replication complex. SUUR loads onto replication forks shortly after the origin firing and participates in chromatin maintenance rather than its establishment. Thus, our findings provide comprehensive evidence that late replication in Drosophila is caused by the time-consuming process of replication-coupled repressive chromatin renewal. Examination of H3K27me3 histone modification in 3 cell types in presence or absence of SuUR mutation.

2016-01-10 | E-GEOD-74908 | biostudies-arrayexpress

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Project description:ChiP-seq profiling of Drosophila melanogaster salivary glands to identify targets for NSL1 and MCRS2.

2010-06-25 | E-MTAB-214 | biostudies-arrayexpress

Chromatin IP of POF, HP1 and H3K9ac and transcript profiling in S2 cells and salivary glands

Project description:Two chromosome-targeting and gene regulatory systems are present in Drosophila melanogaster. The male X-chromosome is targeted by the male-specific lethal complex believed to mediate the two-fold up-regulation of the X-linked genes. The highly heterochromatic 4th chromosome is specifically targeted by the Painting of Fourth (POF) protein which together with heterochromatin protein 1 (HP1) modulate the expression level of genes on the 4th chromosome. Here we report high-resolution mapping of POF and HP1 on the 4th chromosome using chromatin immunoprecipitation followed by tiling microarrays (ChIP-chip) in S2 cells and salivary glands. The enrichments are compared to transcript profiles of the two cell types used. POF specifically binds to genes with a strong preference for exons. The POF binding profile correlates to the binding profile of HP1 which in addition displays a typical M-bM-^@M-^\peakM-bM-^@M-^] in the promoter regions of bound genes. POF and HP1 binds to active genes and the binding correlates with levels of transcription and changes in binding levels are paralleled by a comparable change in transcription. Our results provide a high resolution description of the chromosome 4 specific gene regulatory system provided by the combinatorial effects of POF and HP1. This SuperSeries is composed of the following subset Series: GSE8296: Chromatin IP of POF, HP1 and H3K9ac in S2 cells and salivary glands. GSE8297: Transcript profiling in S2 cells and salivary glands. Keywords: SuperSeries Refer to individual Series

2007-10-02 | E-GEOD-8301 | biostudies-arrayexpress

ChIP with anti-H3K27me3 to compare binding in salivary glands of WT and SuUR Drosophila

Project description:ChIP was performed to identify regions of gDNA bound by H3K27me3 in third instar salivary glands of Drosophila WT and SuUR mutants. This demonstrated that H3K27me3 binds differently in under-replicated in SuUR mutant third instar salivary glands.

2011-10-18 | GSE31897 | GEO

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