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1.
Cell ; 187(13): 3338-3356.e30, 2024 Jun 20.
Artículo en Inglés | MEDLINE | ID: mdl-38810644

RESUMEN

Suspended animation states allow organisms to survive extreme environments. The African turquoise killifish has evolved diapause as a form of suspended development to survive a complete drought. However, the mechanisms underlying the evolution of extreme survival states are unknown. To understand diapause evolution, we performed integrative multi-omics (gene expression, chromatin accessibility, and lipidomics) in the embryos of multiple killifish species. We find that diapause evolved by a recent remodeling of regulatory elements at very ancient gene duplicates (paralogs) present in all vertebrates. CRISPR-Cas9-based perturbations identify the transcription factors REST/NRSF and FOXOs as critical for the diapause gene expression program, including genes involved in lipid metabolism. Indeed, diapause shows a distinct lipid profile, with an increase in triglycerides with very-long-chain fatty acids. Our work suggests a mechanism for the evolution of complex adaptations and offers strategies to promote long-term survival by activating suspended animation programs in other species.


Asunto(s)
Diapausa , Animales , Evolución Biológica , Diapausa/genética , Embrión no Mamífero/metabolismo , Fundulidae/genética , Fundulidae/metabolismo , Regulación del Desarrollo de la Expresión Génica , Peces Killi/genética , Peces Killi/metabolismo , Metabolismo de los Lípidos/genética , Proteínas de Peces/genética , Masculino , Femenino
2.
BMC Genet ; 17: 113, 2016 08 02.
Artículo en Inglés | MEDLINE | ID: mdl-27485207

RESUMEN

BACKGROUND: Considerable natural variation for lifespan exists within human and animal populations. Genetically dissecting this variation can elucidate the pathways and genes involved in aging, and help uncover the genetic mechanisms underlying risk for age-related diseases. Studying aging in model systems is attractive due to their relatively short lifespan, and the ability to carry out programmed crosses under environmentally-controlled conditions. Here we investigate the genetic architecture of lifespan using the Drosophila Synthetic Population Resource (DSPR), a multiparental advanced intercross mapping population. RESULTS: We measured lifespan in females from 805 DSPR lines, mapping five QTL (Quantitative Trait Loci) that each contribute 4-5 % to among-line lifespan variation in the DSPR. Each of these QTL co-localizes with the position of at least one QTL mapped in 13 previous studies of lifespan variation in flies. However, given that these studies implicate >90 % of the genome in the control of lifespan, this level of overlap is unsurprising. DSPR QTL intervals harbor 11-155 protein-coding genes, and we used RNAseq on samples of young and old flies to help resolve pathways affecting lifespan, and identify potentially causative loci present within mapped QTL intervals. Broad age-related patterns of expression revealed by these data recapitulate results from previous work. For example, we see an increase in antimicrobial defense gene expression with age, and a decrease in expression of genes involved in the electron transport chain. Several genes within QTL intervals are highlighted by our RNAseq data, such as Relish, a critical immune response gene, that shows increased expression with age, and UQCR-14, a gene involved in mitochondrial electron transport, that has reduced expression in older flies. CONCLUSIONS: The five QTL we isolate collectively explain a considerable fraction of the genetic variation for female lifespan in the DSPR, and implicate modest numbers of genes. In several cases the candidate loci we highlight reside in biological pathways already implicated in the control of lifespan variation. Thus, our results provide further evidence that functional genetics tests targeting these genes will be fruitful, lead to the identification of natural sequence variants contributing to lifespan variation, and help uncover the mechanisms of aging.


Asunto(s)
Drosophila melanogaster/genética , Variación Genética , Genética de Población , Longevidad/genética , Sitios de Carácter Cuantitativo , Animales , Cruzamientos Genéticos , Femenino , Masculino
3.
Cold Spring Harb Protoc ; 2024(3): pdb.prot107747, 2024 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-37100469

RESUMEN

The state of genome-wide chromatin accessibility in cells, tissues, or organisms can be investigated with a technique called assay for transposase-accessible chromatin using sequencing (ATAC-seq). ATAC-seq is a powerful approach for profiling the epigenomic landscape of cells using very low input materials. Analysis of chromatin accessibility data allows for prediction of gene expression and identification of regulatory elements such as potential enhancers and specific transcription-factor binding sites. Here, we describe an optimized ATAC-seq protocol for the preparation of isolated nuclei and subsequent next-generation sequencing from whole embryos and tissues of the African turquoise killifish (Nothobranchius furzeri). Importantly, we provide an overview of a pipeline for processing and analyzing ATAC-seq data from killifish.


Asunto(s)
Secuenciación de Inmunoprecipitación de Cromatina , Cromatina , Peces Killi , Animales , Cromatina/genética , Núcleo Celular , Análisis de Datos
4.
Science ; 367(6480): 870-874, 2020 02 21.
Artículo en Inglés | MEDLINE | ID: mdl-32079766

RESUMEN

Diapause is a state of suspended development that helps organisms survive extreme environments. How diapause protects living organisms is largely unknown. Using the African turquoise killifish (Nothobranchius furzeri), we show that diapause preserves complex organisms for extremely long periods of time without trade-offs for subsequent adult growth, fertility, and life span. Transcriptome analyses indicate that diapause is an active state, with dynamic regulation of metabolism and organ development genes. The most up-regulated genes in diapause include Polycomb complex members. The chromatin mark regulated by Polycomb, H3K27me3, is maintained at key developmental genes in diapause, and the Polycomb member CBX7 mediates repression of metabolism and muscle genes in diapause. CBX7 is functionally required for muscle preservation and diapause maintenance. Thus, vertebrate diapause is a state of suspended life that is actively maintained by specific chromatin regulators, and this has implications for long-term organism preservation.


Asunto(s)
Diapausa/fisiología , Peces Killi/crecimiento & desarrollo , Músculo Esquelético/crecimiento & desarrollo , Complejo Represivo Polycomb 1/metabolismo , Animales , Diapausa/genética , Regulación del Desarrollo de la Expresión Génica , Histonas/metabolismo , Mutación , Complejo Represivo Polycomb 1/genética
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