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Author: Mia
Zebrafish has become the second most commonly used animal model in medical and life science research thanks to its experimental advantages. To date, scientists have completed many landmark studies using zebrafish models. Unfortunately, it lacks a system functional annotation program similar to that found in other animal models. Recently, a large international team of scientists cataloged zebrafish genetic information and constructed the most comprehensive zebrafish genetic data atlas available.
A recent study published in Nature Genetics suggests that researchers in the medical and life sciences will benefit from the most comprehensive map of zebrafish genetic data to date. The atlas will help researchers better study various types of cancer, heart disease and neurodegeneration, and may prompt more researchers to replace mammalian models in experiments.
https://www.nature.com/articles/s41588-022-01089-w
The historical exploits of zebrafish
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Zebrafish is the second most commonly used animal model in medical and life sciences research, and it is an endemic organism that can be used to study embryonic development and mimic human diseases. Why is zebrafish so popular? The popularity of the zebrafish model is due to its experimental advantages: it has convenient gene manipulation tools and a wide range of genetic resources, and it is highly conserved with the genes and mechanisms of disease among humans. Zebrafish grow transparently like embryos and have unusual regenerative properties that allow researchers to gain insight into the human condition, making it an ideal candidate for studying a variety of diseases and disorders.
To date, scientists have completed many landmark studies using zebrafish models. Zebrafish's application in genomic research has uncovered regulatory patterns for chromatin labeling, DNA encoding used by promoters, DNA methylation, and post-transcriptional messenger RNA regulation. Zebrafish single-cell genomics pioneered the application of spatially resolved lineage-specific transcriptomes during development, and comparative genomics predicted conservative regulatory elements and their long-range target genes. In addition, leveraging the ease of use of zebrafish GMOs, automated in vivo imaging and image processing can be upgraded to high throughput, providing validation of human enhancers associated with the predicted disease.
Complete the functional annotations of zebrafish
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Unfortunately, so far, it lacks a system function annotation program similar to that found in other animal models. To address this, the researchers formed the International DANIO-CODE Consortium and created a central repository to store and process zebrafish developmental functional genomic data. The DANIO-CODE Consortium is a team of 27 laboratories that work together to catalog published open data sets and supplement them with newly generated data. This work resulted in 140,000 DNA regions involved in regulating gene expression in zebrafish.
The study, which sampled 1802 samples, each with millions of data points, provides the broadest range of candidate DNA regions for genetic studies of transgenic breeding, development, and disease. The study's paper, published In the journal July 4, it details the DNA elements involved in some of the stages of embryonic development and improves the understanding of genetic equivalence between zebrafish and mice.
The Synteny projection reveals conservation of epigenetic traits between zebrafish and mice. Image source: https://www.nature.com/articles/s41588-022-01089-w
DANIO-CODE functionally annotates the developing zebrafish genome by: (1) collecting all published and generated new genomic data from 38 laboratories worldwide and standardizing metadata annotations; (2) Create and maintain a Single Data Coordination Center (DCC) for the ongoing accumulation and user download of zebrafish genomic data; (3) Develop standardized analysis pipelines to remap all sequencing datasets; (4) Generate an integrated orbital hub that allows visualization with common genome browsers. In addition, DANIO-CODE performs a comprehensive analysis of these datasets to facilitate discovery, classification of functional elements, and determination of developmental dynamics characteristics. Finally, in this study, the researchers applied a new method of comparative analysis of zebrafish and mammalian genomic datasets to reveal the conservatism of the genomic landscape and expand the utility of zebrafish developmental genomics resources.
Research significance and prospects
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Ferenc Mueller, professor of developmental genetics at the University of Birmingham, who led the study, said: "Cataloguing the genetic information of zebrafish is a major breakthrough that could drive some exciting developments in medicine and life sciences in the coming years. ”
Professor Boris Lenhard of Imperial College London and Professor Carsten Daub of Karolinska Institutet have been instrumental in coordinating more than 50 researchers worldwide. The resulting mapping of collaboration demonstrates how a bottom-up cross-border collaborative initiative can have an impact on our research community.
Carsten Daub, who led the data integration, said: "Now, with our new catalog, we are one step closer to having a fully realized map covering the human genome. Such activities will enable researchers around the world to keep pace with new treatments, drugs, and better understand human and animal diseases. This extensive study integrates all separate data sets into a single framework that enables researchers around the world to solve problems that cannot be solved by study alone. ”
Resources:
https://phys.org/news/2022-07-largest-genetic-atlas-zebrafish-breakthrough.html
Note: This article is intended to introduce the progress of medical research and cannot be used as a reference for treatment options. For health guidance, please visit a regular hospital.
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