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Transcriptome analysis of atad3-null zebrafish embryos elucidates possible disease mechanisms

ABSTRACT: Transcriptome analysis of atad3-null zebrafish embryos elucidates possible disease mechanisms

PROVIDER: PRJNA993229 | ENA |

REPOSITORIES: ENA

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Transcriptome analysis of atad3-null zebrafish embryos elucidates possible disease mechanisms

Project description:ATAD3A is a nuclear gene encoding the ATAD3A protein which has diverse roles in the mitochondria, affecting various cellular processes ranging from mitochondrial dynamics and mtDNA maintenance to metabolism pathways and mitochondrial interactions with other organelles. Pathogenic variants in this gene cause neurological diseases in humans with recognizable genotype-phenotype correlations. Using CRISPR/Cas9 genome editing, we generated a knockout (KO) model for the ortholog gene atad3 in zebrafish., in order to further characterize the gene and its role in health and disease. We examined the phenotype, mitochondrial content and mitochondrial activity of the mutant embryos, and compared the transcriptome of wild-type and mutant embryos at 3 days post-fertilization (dpf) via RNAseq. Results were validated by quantitative real-time PCR at 3dpf and 5dpf. Atad3-null zebrafish embryos demonstrated microcephaly, small eyes, pericardial edema and thinning of the musculature, closely correlating with the human disease. Mitochondrial content and activity were reduced. Transcriptome analysis revealed an expected decline in most mitochondrial pathways in the mutant embryos. In addition, we witnessed a global upregulation of cytosolic tRNA synthetases, presumably secondary to mitochondrial stress and possibly endoplasmic reticulum (ER)-stress. Differential expression of select genes was confirmed in fibroblasts from an affected individual. Zebrafish atad3-null embryos can be used as a reliable model of human ATAD3A-associated disorders, as the pathways and processes differentially expressed in this model are similar to the ones in humans. Moreover, our study confirms mitochondrial dysfunction as the primary underlying pathogenic mechanism in ATATD3A-associated disorders.

2025-02-01 | GSE236968 | GEO

Transcriptome analysis of 6 hours post fertilization mecp2-null versus wild type zebrafish embryos

2016-09-01 | GSE80348 | GEO

Transcriptome analysis of 6 hours post fertilization mecp2-null versus wild type zebrafish embryos

Project description:RNA sequencing was performed on RNA isolated from groups of 6 hpf wild type and mecp2-null embryos (n=3 biological replicates per condition with 30 embryos pooled per replicate). DESeq2 analysis was performed using https://usegalaxy.org/ Whole embryo mRNA profile of 30 pooled mecp2-null or wild type 6 hpf zebrafish embryos, in triplicate, using the Illumina HiSeq4000 platform

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Transcriptome changes in Slc7a5-null mouse embryos

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Altered basal and TCDD-induced gene expression in zebrafish embryos made AHRRa-null by ZFN-mediated gene targeting

Project description:The aryl hydrocarbon receptor (AHR) repressor (AHRR), a bHLH-PAS protein, is a transcriptional repressor of AHR and other transcription factors (HIF, ER) and is regulated by an AHR-dependent mechanism. However, the physiological and toxicological roles of AHRR are not well understood. We demonstrated earlier that knockdown of AHRRa (one of two AHRR paralogs) in zebrafish embryos using morpholino anti-sense oligonucleotides results in developmental phenotypes such as pericardial edema, craniofacial malformations, and cardiac deformities, similar to effects caused by exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). AHRRa morphants also exhibit down-regulation of genes associated with photoreceptor development. To characterize the AHRRa function further, we used ZFN (zinc finger nuclease) technology to generate a line of zebrafish with a 7-bp deletion in exon 3 of AHRRa, leading to a truncated AHRR (110 aa, of which 38 are from AHRRa, compared to the 550-aa wild-type (wt) AHRRa). The mutant AHRRa protein, which contains basic regions but lacks the HLH and PAS domains, did not repress AHR in vitro, suggesting that it is inactive (null). Unlike AHRRa morphants, AHRRa-null fish did not display a TCDD-like phenotype; exposure to TCDD caused defects similar to those in TCDD-exposed wt embryos. RNA-sequencing revealed that basal expression of 562 genes differed significantly between the null and wt embryos, including down-regulation of genes associated with photoreceptor development, as seen in AHRRa morphants. TCDD-induced gene expression patterns for the prototypic AHR target genes were similar for null and wt embryos. However, 22 genes were differentially regulated by TCDD in the AHRRa-null embryos as compared to wt embryos (>2-fold; 5% FDR). We are currently investigating the link between these differentially expressed genes and the function of AHRRa in development and AHR signaling. [Supported by NIH R01ES006272]

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Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic

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Comparative transcriptomic analysis between wild-type (WT) and Cables2-null embryos.

Project description:We found that conventional targeted disruption of the entire Cables2 locus caused post-gastrulation embryonic lethality in mouse. To examine global gene changes during gastrulation, we performed the RNA-seq experiment using WT- and Cables2-null embryos at embryonic day 6.5 and 7.5.

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Transcriptome analysis identifies genes dysregulated in Sox7-null embryos at E8.5

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