Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigation of genetic compensation in tdp1-/- zebrafish embryos

ABSTRACT: Investigation of genetic compensation in tdp1-/- zebrafish embryos

PROVIDER: PRJNA626551 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Investigation of genetic compensation in tdp1-/- zebrafish embryos

Project description:Tdp1, tyrosyl-DNA phosphodiesterase 1, is an enzyme responsible for the repair of DNA breaks resulting from aberrant topoisomerase 1 activity, called Top1 cleavage complexes (Top1-CCs). Mutation of Tdp1 leads to a progressive neurodegenerative disorder spinocerebellar ataxia with axonal neuropathy 1 (SCAN1). We have generated tdp1-/- zebrafish as a model for SCAN1. The adult fish have a behavioral defect and hypersensitivity to camptothecin (CPT), a Top1 poison. Strikingly, the embryos do not show increased sensitivity to CPT, unlike any other reported vertebrate models, suggesting genetic compensation is at play at this stage. We thus carried out microarray analysis in CPT-treated zebrafish embryos to compare the gene expression profiles of tdp1WT and tdp1-/- genotypes. Gene expression analysis revealed 1,8111 genes that were differentially expressed: 1,071 were upregulated and 740 were downregulated. Sprtn and neil1, two potential compensation candidates were upregulated in the tdp1-/- embryos.

2022-04-19 | GSE148923 | GEO

Genetic compensation in a stable slc25a46 mutant zebrafish

Project description:Genetic compensation in a stable slc25a46 mutant zebrafish

| PRJNA575769 | ENA

Genetic compensation in a stable slc25a46 mutant zebrafish

Project description:A phenomenon of genetic compensation is commonly observed when an organism with a disease-bearing mutation does not show phenotypic penetrance due to compensatory gene expression changes. Reports have spread showing the absence of disease phenotypes in stable knockout models, but not in transient knockdown models. As such, these incidents present a challenge for the disease modeling field, although a deeper understanding of genetic compensation may also hold the key for novel therapeutic interventions. In our study we created a knockout model of slc25a46 gene, which is a recently discovered important player in mitochondrial dynamics and deleterious mutations in which are known to cause peripheral neuropathy, optic atrophy and cerebellar ataxia. We report a case of genetic compensation in the fourth generation (F4) of slc25a46 knockout zebrafish mutant, in contrast to a penetrant disease phenotype in the first generation (F0) slc25a46 mosaic mutant (crispant), generated with CRISPR/Cas-9 technology. We show that F0 crispant phenotype is specific and rescuable. By performing mRNA sequencing, we define significant changes in slc25a46 F4 mutant’s gene expression profile, which are nearly not present in F0 crispants. We find that among the top candidates for the phenotypic compensation anxa6 gene stands out as a functionally relevant player in mitochondrial dynamics. We also find that our genetic compensation case does not arise from previously identified mechanisms driven by mutant mRNA decay. Our study serves as an important contribution to the understanding of phenomenon of genetic compensation and presents novel insights on Slc25a46 function. Furthermore, our study provides the evidence for the efficiency of F0 CRISPR screens for disease candidate genes, which may advance the field of functional genetics.

2019-10-04 | GSE138414 | GEO

Gene expression profiling of MeCP2 deficient zebrafish embryos

Project description:Investigation of whole genome gene expression level changes in mecp2 morphant zebrafish embryos as compared to wild-type strain.

2015-07-21 | GSE71173 | GEO

Proteomics of SEMA5A, MT-ATP6, ZNF662, and KDM4C in zebrafish embryos

Project description:Proteomics of SEMA5A, MT-ATP6, ZNF662, and KDM4C in zebrafish embryos

2024-02-05 | PXD049175 | iProX

X-chromosome dosage compensation dynamics in human early embryos

Project description:Studying X-chromosome dosage compensation dynamics in human early embryos using single cell RNA sequencing

2019-10-24 | GSE130050 | GEO

Zebrafish embryo Kac - Global proteomic analysis of lysine acetylation in zebrafish (Danio rerio) embryos

Project description:Zebrafish (Danio rerio) model system have used widespread vertebrate investigations for genetic and cell biological analyses, and is suitable for small molecular screens such as chemical, toxicity and drug in order to use for human diseases and drug discovery . Recently, These powerful zebrafish model increasingly apply to human metabolic disease such as obesity and diabetes and toxicology. Despite a lot of advantages, proteomics research at zebrafish has received little interest in comparison with genetic and biological research using histology and in situ hybridization. Protein lysine acetylation is one of the most known post-translational modifications with dynamic and reversibly controlled by lysine acetyltransferase such as histone acetyltransferases and lysine deacetylase such as histone deacetylases and sirtuins family.Also, during the past year, global lysine acetylome studies using MS-based proteomics approach was in diverse species such as human, mouse, E. coli, Yeast and plants. Based on global acetylome data, our understanding of the roles of lysine acetylation in various cellular processes has increased. . The aim of this study was to identify Lysine acetylation in zebrafish embryos and determine the homology from Human at modified site level. Here we showed the global lysine acetylation study in Zebrafish embryos using MS-based zebrafish embryos.

2016-10-10 | PXD003455 | Pride

Expression analysis of zebrafish TIF1g-deficient, cdc73 deficient and double-deficient embryos

Project description:Investigation of whole genome gene expression level changes in zebrafish TIF1g-deficient, cdc73 deficient and double-deficient embryos, compared to the wild-type ebryos.

2010-07-13 | GSE20432 | GEO

An Investigation into the Biological Effects of Indirect Potable Reuse Water Using Zebrafish Embryos

Project description:An Investigation into the Biological Effects of Indirect Potable Reuse Water Using Zebrafish Embryos

| PRJNA638388 | ENA

Expression analysis of zebrafish TIF1g-deficient, cdc73 deficient and double-deficient embryos

Project description:Investigation of whole genome gene expression level changes in zebrafish TIF1g-deficient, cdc73 deficient and double-deficient embryos, compared to the wild-type ebryos. A twelve-chip study using total RNA isolated from gata1-GFP positive cells (sorted by FACS) from 12 somite-stage wild type embryos, TIF1g morholino injected, Cdc73 morpholino injected and double morpholino injected embryos.

2010-07-13 | E-GEOD-20432 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data