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RNA-seq profiling of Drosophila larval ring glands of kdm5 null mutants

ABSTRACT: kdm5 is an essential gene in Drosophila that has critical developmental roles in the prothoracic gland cells of the larval ring gland. We performed a bulk transcriptome analysis of the larval ring gland in w[1118] (wild type) and kdm5[140] (null mutant) in order to identify genes in the prothoracic gland involved in the lethality of kdm5 null mutants. We found that the absence of kdm5 causes dysregulation of genes involved in various metabolic pathways. In particular, genes both bound by KDM5 and differentially expressed in this cell type are involved in regulation of mitochondrial biology and autophagy.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE229075 | GEO | 2023/10/16

REPOSITORIES: GEO

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Genome-winding binding profile of KDM5 in Drosophila larval prothoracic gland cells via Targeted DamID analysis

Project description:kdm5 is an essential gene in Drosophila that has critical developmental roles in the prothoracic gland cells of the larval ring gland. To profile KDM5 binding within these cells and this developmental stage, we performed Targeted DamID (TaDa). By profiling the nearest genes to significant TaDa peaks (FDR < 0.01), we identified 5815 candidate KDM5 target genes. Interestingly, 42% of these candidate KDM5 target genes appear to be conserved across multiple cellular contexts in Drosophila and span many cellular processes for future investigation.

2023-10-16 | GSE229076 | GEO

Transcriptome analysis of Drosophila melanogaster third instar larval ring glands points to novel functions and uncovers a cytochrome p450 required for development

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2016-11-27 | GSE76304 | GEO

RNA-seq analysis of de larval ventral nerve cord (VNC) from kdm5[L854F] and enzymatically inactive kdm5[JmjC*]

Project description:We performed a transcriptome analysis of the larval VNC in kdm5 WT, kdm5[L854F] and enzymatically inactive kdm5[JmjC] in order to identify genes contributing to the phenotypes observed in the mutants' neuromuscular junction (NMJ). We found that inactivation of the catalytic activity in kdm5[JmjC] causes dysregulation of genes related to glutamate metabolism while the mutation L854F leads to dysregulation of genes involved in microtubule cytoskeleton dynamics. We also found a group of genes dysregulated in both mutants that likely explain a common NMJ phenotype.

2021-03-16 | GSE159298 | 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

Proteomic analysis of Bombyx mori prothoracic glands from day 0 and day 6 of the 5th instar

Project description:The project aim was to identify the proteins expressed by the prothoracic gland cells during the final larval stage of the model insect, Bombyx mori.

2016-06-08 | PXD004265 | Pride

Proteomic analysis of prothoracic glands of the silkworm Bombyx mori

Project description:The project aim was to identify the cell membrane receptors that prothoracic gland cells use to decode and transduce information from the extracellular environment during the final larval stage of the model insect, Bombyx mori.

2016-01-27 | PXD002771 | Pride

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[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

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

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