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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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LID ChIP-Seq in wild type, and H3K4me3 ChIP-Seq in wild type and lid RNAi Drosophila melanogaster

ABSTRACT: 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. Analysis of LID-binding sites in wild type, and of H3K4me3-binding sites in wild type and LID RNAi wing imaginal discs.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: David Rossell

PROVIDER: E-GEOD-27078 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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dKDM5/LID regulates H3K4me3 dynamics at the transcription-start site (TSS) of actively transcribed developmental genes.

Lloret-Llinares Marta M Pérez-Lluch Sílvia S Rossell David D Morán Tomás T Ponsa-Cobas Joan J Auer Herbert H Corominas Montserrat M Azorín Fernando F

Nucleic acids research 20120816 19

H3K4me3 is a histone modification that accumulates at the transcription-start site (TSS) of active genes and is known to be important for transcription activation. The way in which H3K4me3 is regulated at TSS and the actual molecular basis of its contribution to transcription remain largely unanswered. To address these questions, we have analyzed the contribution of dKDM5/LID, the main H3K4me3 demethylase in Drosophila, to the regulation of the pattern of H3K4me3. ChIP-seq results show that, at ...[more]

PMID: 22904080

Similar Datasets

Drosophila dKDM5/LID regulates H3K4me3 dynamics at the transcription start site of actively transcribed developmental genes

Project description:This SuperSeries is composed of the following subset Series: GSE26895: Drosophila LID RNAi gene expression profiling GSE27078: LID ChIP-Seq in wild type, and H3K4me3 ChIP-Seq in wild type and lid RNAi Drosophila melanogaster GSE40599: POLIISER5 and POLIISER2 ChIP-Seq in mutant RNAi LID Drosophila Melanogaster Refer to individual Series

2012-08-30 | E-GEOD-27081 | biostudies-arrayexpress

POLIISER5 and POLIISER2 ChIP-Seq in mutant RNAi LID Drosophila Melanogaster

Project description: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 POLIISER5 and POLIISER2 are localized in LID RNAi mutants. 1 sample for POLIISER5 with an input control, and 1 sample for POLIISER2 with an input control.

2012-09-04 | E-GEOD-40599 | biostudies-arrayexpress

Drosophila LID RNAi gene expression profiling

Project description:H3K4me3 is a histone modification related to gene activation. LID is a demethylase acting on this residue and therefore, it could be important for proper expression of genes in Drosophila developing tissues, such as wing imaginal discs We used microarrays to analyse the changes in gene expression after lid depletion by RNAi, both in a wild type background and in a mutant background Two replicates were obtained on Nov 2010 for wild type white drosophila, GFP RNAi control and LID RNAi (on a LID mutant background).

2012-08-30 | E-GEOD-26895 | biostudies-arrayexpress

LID ChIP-Seq in wild type, and H3K4me3 ChIP-Seq in wild type and lid RNAi Drosophila melanogaster

Project description: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.

2012-08-30 | GSE27078 | GEO

Drosophila LID RNAi gene expression profiling

2012-08-30 | GSE26895 | GEO

POLIISER5 and POLIISER2 ChIP-Seq in mutant RNAi LID Drosophila Melanogaster

2012-09-04 | GSE40599 | GEO

H3K4me3 modification profiling of Huntingtons disease and control human post-mortem prefrontal cortex brain samples

Project description:Huntingtonâs disease (HD) is an autosomal-dominant neurodegenerative disorder resulting from expansion in the number of CAG repeats in the coding region of exon 1 of the Huntingtin (HTT) gene. One of the most widely studied chromatin modifications is trimethylated lysine 4 of histone 3 (H3K4me3). Here, we conducted the first comprehensive study of H3K4me3 ChIP-sequencing in neuronal chromatin from the prefrontal cortex of six HD cases and six non-neurologic controls. We examined two classes of H3K4me3 peaks; those located near transcription start sites (TSSs) (termed âproximalâ) and those located distantly from TSSs (termed âdistalâ). We detected 2,830 differentially enriched H3K4me3 peaks between HD and controls, with 55% of them down regulated in HD. We found an unexpected discordance between levels of H3K4me3 and mRNA, with H3K4me3 predominantly reduced in HD and mRNA predominantly increased in HD. Gene ontology (GO) term enrichment analysis of the genes associated with the proximally positioned peaks, revealed diverse biological process terms with organ morphogenesis and positive regulation of gene expression most frequently implicated. GO terms relating to transcription and the extracellular matrix were also observed. Approximately 36% of the distal peaks co-localized to enhancer sites, with six transcription factors and chromatin remodelers differentially enriched in HD H3K4me3 distal peaks, including EZH2 and SUZ12, two core subunits of the polycomb repressive complex 2 (PRC2). Moreover, sequences repressed by polycomb in normal frontal cortex were significantly depleted in HD-enriched peaks, suggesting that H3K4me3 histone hypermethylation is linked to dysregulated polycomb activity in the HD neuronal epigenome. 12 H3K4me3 ChIP-seq libraries (6 Huntington's disease, 6 neurologically normal control), and 1 input DNA library (neurologically normal control)

2015-12-14 | E-GEOD-68952 | biostudies-arrayexpress

Transcriptome analysis upon SIN3 or dKDM5/LID knockdown or both under normal and paraquat induced stress conditions in Drosophila S2 cultured cells

Project description:SIN3 the scaffold protein of a histone deacetylase complex interacts with a histone demethylase KDM5 (little imaginal discs - LID) in Drosophila. Reduction of SIN3 or dKDM5/LID both result in similar phenotypes during cell proliferation and wing development. To identify underlying transcriptional changes that may contribute to these phentypic defects we performed whole genome expression analysis in Drosophila cultured cells upon RNAi-mediated knockdown of Sin3A, lid or both. We identified a large number of genes regulated by SIN3, dKDM5/LID or both. While many common genes were regulated by SIN3 and dKDM5/LID an enrichment for genes involved in stress tolerance pathways was observed. Additional RNAseq analysis of expression changes upon knockdown of Sin3A, lid or both under paraquat mediated oxidative stress conditions identified significant changes in genes involved in cell cycle related processes. Drosophila S2 cells were treated with dsRNA targetting Sin3A, lid and both or GFP as control under normal or oxidative stress conitions induced by treatment with paraquat. mRNA profiling of these samples were performed by deep sequencing using Illumina Hiseq2500.Three biological replicates were performed.

2016-01-09 | E-GEOD-68775 | biostudies-arrayexpress

H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence (ChIP-seq)

Project description:Cellular senescence is a tumor-suppressive program that involves chromatin reorganization and specific changes in gene expression that trigger an irreversible cell-cycle arrest. We combined quantitative mass spectrometry and ChIP deep-sequencing to identify changes in histone modification occurring during cellular senescence. ChIP-seq was carried out using H3K4me3-specific antibodies in growing, quiescent, senescent, or senescent with shRB targeting Rb, IMR90 cells. The control mock data (ChIP-seq using anti-mouse IgG antibody) is available in GEO Sample GSM497500 (Series GSE19898).

2013-01-31 | E-GEOD-43921 | biostudies-arrayexpress

BRWD3 targets KDM5/Lid for degradation to maintain H3K4 methylation levels

Project description:Histone modifications are critical for regulating chromatin structure and gene expression. Dysregulation of histone modification levels may contribute to disease development and cancer. Therefore, understanding histone modifications is essential for development and disease. The chromatin-binding protein BRWD3, a known substrate-specificity factor of the Cul4-DDB1 E3 ubiquitin ligase complex, is required for maintaining active histone modification levels. Loss of BRWD3 function causes an increase in H3K4me1 levels. The underline mechanism, however, is unknown. We found that BRWD3 depletion also causes a decrease in H3K4me3 levels. To reveal the mechanism by which BRWD3 regulates the H3K4 methylation levels, we performed BRWD3-IP mass-spectrometry. We identified an interaction between BRWD3 and the lysine-specific demethylase 5 (KDM5/Lid), an enzyme that removes tri- and di- methyl marks from lysine 4 on histone H3. Moreover, analysis of ChIP-seq data revealed that BRWD3 and KDM5 are significantly co-localized throughout the genome. We show that BRWD3 promotes K48-linked ubiquitination of KDM5. Consistent with this, KDM5/Lid is rapidly degraded in a proteasome-dependent manner with a half-life of less than 30 mins. Critically, KDM5/Lid degradation is dependent on both BRWD3 and Cul4. In addition, we have found that BRWD3 is suppressor of Position-effect variegation (PEV). Loss of a single copy of KDM5, however, partially rescues the the BRWD3 PEV phenotype. Our results suggest that BRWD3 targets KDM5/Lid for degradation to ensure the balance of H3K4me levels.

2023-09-19 | PXD039706 | Pride

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