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Circular RNAs in the ageing African turquoise killifish

ABSTRACT: Circular RNAs in the ageing African turquoise killifish

PROVIDER: PRJNA553674 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9665480_1.fastq.gz	Fastqsanger.gz
	SRR9665480_2.fastq.gz	Fastqsanger.gz
	SRR9665481_1.fastq.gz	Fastqsanger.gz
	SRR9665481_2.fastq.gz	Fastqsanger.gz
	SRR9665482_1.fastq.gz	Fastqsanger.gz

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Circular RNAs in the ageing African turquoise killifish

Project description:In this work we took 9 samples from brain and 6 samples from muscle of the African turquoise killifish (Nothobranchius furzeri) at 3.5, 8.5 and 14 weeks. Total RNA was sequenced and circRNAs were detected.

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Identification of retinal cell types within the ageing African turquoise killifish retina and their respective age-related transcriptional changes using scRNA-seq

Project description:The mammalian central nervous system (CNS) and its retina are susceptible to age-related patholgoies, resulting in progressive, irreversible diseases like glaucoma and age-related macular degeneration (AMD), which are increasingly prevalent with rising life expectancy. Currently, there are no targeted long-term therapies to prevent vision loss. The short lived African turquoise killifsh (Nothobranchius furzeri, GRZ-AD) is a valuable genetic model for ageing studies, displaying rapid ageing phenotypes within its four to six-month lifespan. Our investigation on the molecular consequences of ageing in the retina, employing scRNA-sequencing, shows a a comprehensive overview of the cellular heterogeneity of the killifish retina, uncovering age-related gene expression changes specific to certain retinal cell populations.

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Effect of ageing on gene expression in the African turquiose killifish retina

Project description:The mammalian central nervous system (CNS) is susceptible to age-related pathologies, resulting in progressive, irreversible disease. Neurodegenerative eye conditions, like glaucoma and age-related macular degeneneration (AMD), are on the rise due to increased life expectancy. Despite this, there are currently no long-term therapies to prevent degeneration and vision loss. The short-lived African turquoise kililfsh (Nothobranchius furzeri GRZ-AD) is an ideal genetic model for ageing studies, exhibiting rapid ageing phenotypes within its four to six-mont lifespan. Investigating the molecular consequences of ageing in the retina, we conducted bulk RNA-sequencing, revealing dysregulation of genetic pathways associated with ageing CNS and retinal diseas in the aged killifish retina.

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Identification of retinal cell types within the ageing African turquoise killifish retina and their respective age-related transcriptional changes using scRNA-seq

Project description:Identification of retinal cell types within the ageing African turquoise killifish retina and their respective age-related transcriptional changes using scRNA-seq

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Effect of ageing on gene expression in the African turquiose killifish retina

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Evolution of diapause in the African killifish by remodeling ancient gene regulatory landscape

Project description:Suspended animation (e.g. hibernation, diapause) allows organisms to survive extreme environments. But the mechanisms underlying the evolution of suspended animation states are unknown. The African turquoise killifish has evolved diapause as a form of suspended development to survive the complete drought that occurs every summer. Here, we show that gene duplicates – paralogs – exhibit specialized expression in diapause compared to normal development in the African turquoise killifish. Surprisingly, paralogs with specialized expression in diapause are evolutionarily very ancient and are present even in vertebrates that do not exhibit diapause. To determine if evolution of diapause is due to the regulatory landscape rewiring at ancient paralogs, we assessed chromatin accessibility genome-wide in fish species with or without diapause. This analysis revealed an evolutionary recent increase in chromatin accessibility at very ancient paralogs in African turquoise killifish. The increase in chromatin accessibility is linked to the presence of new binding sites for transcription factors, likely due to de novo mutations and transposable element (TE) insertion. Interestingly, accessible chromatin regions in diapause are enriched for lipid metabolism genes, and our lipidomics studies uncover a striking difference in lipid species in African turquoise killifish diapause, which could be critical for long-term survival. Together, our results show that diapause likely originated by repurposing pre-existing gene programs via recent changes in the regulatory landscape. This work raises the possibility that suspended animation programs could be reactivated in other species for long-term preservation via transcription factor remodeling and suggests a mechanism for how complex adaptations evolve in nature.

2021-08-05 | ST001898 | MetabolomicsWorkbench

Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish

Project description:Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish

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Chromosome conformation capture (Hi-C) of the turquoise killifish

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Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish II.

Project description:Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish II.

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Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish I.

Project description:Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish I.