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Genome-wide maps of KDM5 binding in drosophila adults

ABSTRACT: To determine which genes affected by loss of KDM5 in adults were direct targets, we carried out KDM5 ChIP-seq analyses. To valide this data, we utilized a previously generated fly strain in which the sole source of KDM5 is from a transgene expressing an HA tagged form of KDM5 expressed under the control of its endogenous promoter. Comparing genome-wide gene expression and KDM5 binding analyses in Drosophila adults, we demonstrate the primary function of KDM5 in adults is to activate gene expression KDM5. To investigate the link between KDM5 and H3K4me3, we carried out anti-H3K4me3 ChIP-seq from wildtype adults . Genome-wide, KDM5 and H3K4me3 peaks showed a similar distribution, with both peaking at the transcription start site (TSS) showed a striking overlap with the presence of H3K4me3.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE70589 | GEO | 2015/12/22

SECONDARY ACCESSION(S): PRJNA289118

REPOSITORIES: GEO

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Genome-wide maps of KDM5 binding in drosophila adults

Project description:To determine which genes affected by loss of KDM5 in adults were direct targets, we carried out KDM5 ChIP-seq analyses. To valide this data, we utilized a previously generated fly strain in which the sole source of KDM5 is from a transgene expressing an HA tagged form of KDM5 expressed under the control of its endogenous promoter. Comparing genome-wide gene expression and KDM5 binding analyses in Drosophila adults, we demonstrate the primary function of KDM5 in adults is to activate gene expression KDM5. To investigate the link between KDM5 and H3K4me3, we carried out anti-H3K4me3 ChIP-seq from wildtype adults . Genome-wide, KDM5 and H3K4me3 peaks showed a similar distribution, with both peaking at the transcription start site (TSS) showed a striking overlap with the presence of H3K4me3. Examination of KDM5 binding and histone H3K4me3 modifications in drosophila adults

2015-12-22 | E-GEOD-70589 | biostudies-arrayexpress

RNA-seq analyses of kdm5 mutant flies and wt flies under normal condition and oxidative stress

Project description:Comparing the transcriptome of wildtype and kdm5 mutant flies in normal conditions revealed a total of 4787 genes that were significantly downregulated and thus require KDM5 for their activation, and 3269 upregulated genes that are normally repressed by KDM5 (p<0.05, FDR <0.05). Because kdm5 mutants are sensitive to the oxidizer paraquat, we also carried out RNA-seq from wildtype and kdm5 mutant adults in oxidative stress conditions. Paraquat treatment of wildtype flies lead to the upregulation of 2481, and downregulation of 3103 genes adult mRNA profiles of 1-3-days old wild type (WT) and kdm5 mutant under normal condition and oxitative stress were generated by deep sequencing, using Illumina HisSeq 2000.

2015-12-22 | E-GEOD-70590 | biostudies-arrayexpress

RNA-seq analyses of kdm5 mutant flies and wt flies under normal condition and oxidative stress

2015-12-22 | GSE70590 | GEO

RNA-seq analysis of kdm5 null mutant wing discs

Project description:In order to determine which genes were affected by the complete loss of kdm5, we carried out RNA-seq analysis using wing discs from wildtype and kdm5 140, the new null mutant. Consistent with the phenotypes observed, transcriptome analyses of kdm5140 mutant wing imaginal discs revealed the dysregulation of a significant number of genes involved in cell cycle progression and DNA repair.

2019-12-31 | GSE109201 | GEO

H3K4me3 ChIP in multiple myeloma MM1S cells in the presence and absence of KDM5-C70

Project description:In this experiment we demonstrate the use of an inhibitor of the KDM5 family of histone demethylases, KDM5-C70, on H3K4me3 marks in the multiple myeloma cell line MM1S. KDM5-C70 increases H3K4me3 in a global fashion across the genome. Examination of H3K4me3 mark across MM1S cells treated with either KDM5-C70 or vehicle control

2016-04-05 | E-GEOD-78206 | biostudies-arrayexpress

RNA-seq analyses of kdm5[A512P] and enzymatically inactive kdm5[JmjC*] in adult heads

Project description:The goal of this study was to generate a Drosophila model of intellectual disability caused by mutations in kdm5. RNA-seq was used to define the transcriptional defects of a mutation in Drosophila that is analogous to a human intellectual disability-associated allele, kdm5[A512p]. These data revealed a total of 1609 dysregulated genes, 778 of which were upregulated and 831 were downregulated. To determine whether these transcriptional defects were due to the loss of KDM5-induced histone demethylation, we also carried out RNA-seq from a enzymatic inactive strain, kdm5[Jmjc*]. These data revealed a striking similarity between the two datasets and suggest that the primary defect of KDM5[A512P] is loss of histone demethylase activity.

2018-12-31 | GSE100578 | GEO

Gut microbiota analysis of kdm5 mutant and the flies with KDM5 knockdown in intestine tissue

Project description:To determine microbiota composition associated with loss of KDM5 in intestine, we carried out 16S rRNA seq analyses of dissected intestine from wildtype and kdm5 mutant. [GSM2628181-GSM2628190]. A total of 78 operational taxonomic units (OTUs) were identified in the sequence data. There were about 15 genera much less abundant in kdm5 mutant compared to wildtype. The kdm5 mutant were sensitive to pathogen. To confirm the microbiota associated with loss of KDM5 in intestine, 16S rRNA of new flies were sequenced and analyzed by Majorbio Bio-Pharm Technology Co. Ltd. (Shanghai, China) [GSM3243472-GSM3243481]. A total of 107 operational taxonomic units (OTUs) were identified in the sequence data. There were about 20 genera much less abundant in kdm5 mutant compared to wildtype. To confirm the microbiota associated with loss of KDM5 drosophila feeding with Lactobacillus plantarum, 16S rRNA of kdm5 mutant flies were sequenced and analyzed by Novogene Bioinformatics Technology Co., Ltd. (Tianjin, China) [GSM3263522-GSM3263527]. A total of 92 operational taxonomic units (OTUs) were identified in the sequence data. To confirm the microbiota associated with KDM5 knockdown in intestine, 16S rRNA of Myo1A-Gal4TS/+ and Myo1A-Gal4TS/+;+/kdm5RNAi flies were sequenced and analyzed by Biomarker Co. Ltd. (Beijing, China). [GSM3507915-GSM3507924]. A total of 50 operational taxonomic units (OTUs) were identified in the sequence data. There was a significant different based on the genus level between two groups.

2019-02-08 | GSE98944 | GEO

H3K4me3 ChIP in multiple myeloma MM1S cells in the presence and absence of KDM5-C70

2016-04-05 | GSE78206 | GEO

The gene expression changes associated with loss of KDM5 (lid) in Drosophila wing discs

Project description:To determine the gene expression changes associated with loss of KDM5, we carried out microarray analyses of dissected wing imaginal discs from wildtype (w1118) and kdm510424 homozygous mutant 3rd instar larvae (96hr AED). kdm510424 is >99% homozygous lethal and we are unable to detect KDM5 protein by Western blot, thus it is likely to be a strong loss-of-function allele. Hierarchical cluster analysis of our microarray data revealed that of the 18,500 transcripts represented on the array, 367 genes were up-regulated and 534 genes were down-regulated 1.5-fold or more in kdm5 mutants compared to wildtype (p<0.05). To highlight biological processes potentially regulated by KDM5, we determined which gene ontology (GO) terms were enriched within the differentially expressed genes. While a total of ten GO terms were significantly enriched (p<0.01), two functionally related and overlapping terms clearly had the largest number of genes: (1) response to stress and (2) oxidation reduction.

2014-12-31 | GSE53881 | GEO

KDM5 histone demethylases repress innate immune response via suppression of STING

Project description:Tri-methylation on histone H3 lysine 4 (H3K4me3) is enriched near transcription start sites and correlates with active transcription. Like other histone marks, methylation on H3K4 is catalyzed by the respective methyltransferases and erased by demethylases. Lysine demethylase 5 (KDM5) family of Fe (II) and α-ketoglutarate-dependent dioxygenases removes the methyl groups from H3K4me3. All four family members of KDM5 demethylases (KDM5A-D) share sequence identity, have similar in vitro kinetic parameters, and display functional redundancy. To determine the effects of complete depletion of KDM5 activity, we treated MCF7 cells with DMSO, or two pan-KDM5 specific inhibitors, KDM5-C70 (our lab code 443) and CPI-48 (our lab code 278) and performed RNA sequencing to determine gene expression changes after KDM5 inhibitor treatment.

2018-07-03 | GSE108502 | GEO

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