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Fishing for solutions

Examining function of all genes in the zebrafish genome to benefit human health

2013-04-18
(Press-News.org) Equipped with the zebrafish genome, researchers have designed a method to assay the function of each and every gene and to explore the effects genetic variation has on zebrafish. So far the team has generated one or more mutations in almost 40% of all zebrafish genes.

The resource will be a comprehensive catalogue of how changes to our genes can have physical and biochemical consequences, giving other researchers the tools to understand human disease. Many genes are similar between the human genome and those of less complex animals. As a vertebrate, the zebrafish (Danio rerio) has the same major organs and tissues as humans.

For example, their muscle, blood, kidney and optical structures share many features with the human systems. Zebrafish embryos are transparent, so researchers can easily study their development. Zebrafish share 70% of genes with humans and 84% of genes known to be associated with human disease have a zebrafish counterpart.

"There are several advantages of the zebrafish model," says Dr Leonard Zon, MD, Children's Hospital of Boston MA. "We can readily create variations in their genome that are relevant to human health and disease. This has allowed a greater understanding of gene function and the finding of new targets for drug treatments.

"Several small molecules discovered using the zebrafish system have recently entered into clinical trials. The availability of the genome sequence, coupled with the rapid expansion of disease models and chemical screening ability, ensures that the zebrafish system has a major place in biomedicine."

The high-quality zebrafish reference genome sequence reported today in Nature, has allowed the team to create different mutations in more than 10,000 genes. There are 5,494 genes known to be involved in human disease. So far, the team have identified mutations in 3,188 zebrafish gene counterparts of the 5,494 genes associated with human disease.

Based on traditional methods used to study zebrafish, the team developed a new approach to more efficiently find the consequences of genetic variation in the zebrafish. They create random mutations throughout the genome of the zebrafish and link the mutations to physical or biochemical changes.

"Our aim is to reveal the function of each gene in the zebrafish to shed light on the role of their human counterpart," says Dr Elisabeth Busch-Nentwich, first author from the Wellcome Trust Sanger Institute. "We make these zebrafish models freely available to the wider scientific and medical communities to support their effort to understand human disease and increase the pace at which medical advancements can be made."

A previous study at the Institute found specific mutations in the gene Titin are potential drivers for the growth of some forms of cancer. The team found that the main function of this gene in zebrafish may be associated with the division of cells in the body. This would explain why changes to this gene can affect the way cells divide and can be a driving force in the growth of cancer. "Our zebrafish models have already been used to confirm the identity of a gene responsible for a rare disease affecting the development of bones," says Dr Ross Kettleborough, first author from the Wellcome Trust Sanger Institute. "This is just one of many examples where this project has and will advance our understanding of human disease."

Zebrafish have already played a central role in helping to unravel the biological processes behind muscular dystrophies and are an important model for unlocking the mechanisms of cancer and other diseases. This project will help to uncover the biological processes that underlie both common and rare diseases, point to the causal genes and may lead to new treatments.

"Our challenge is to develop a comprehensive, functional understanding of all human genes as quickly as possible," says Dr Derek Stemple, lead author from the Wellcome Trust Sanger Institute. "Our systematic analysis of zebrafish gene function will advance understanding of human disease."

"This is a resource that will help researchers and clinicians find the gene variations responsible for our inheritance of, and susceptibility to, diseases."

### Notes to Editors Publication Details Ross N. W. Kettleborough, Elisabeth M. Busch-Nentwich, Steven A. Harvey et al. (2013) 'A systematic genome-wide analysis of zebrafish protein-coding gene function' Advanced online publication in Nature, 17 April DOI: 10.1038/nature11992

Funding A full list of funding can be found in the paper

Participating Centres 1. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK 2. MRC-CDBG/Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield, S10 2TN, UK 3. Hubrecht Institute, KNAW and University Medical Center Selected Websites With nearly 25,000 of the brightest students from 117 countries coming to learn alongside 1,209 of the world's best academics, it is clear why the University of Sheffield is one of the UK's leading universities. Staff and students at Sheffield are committed to helping discover and understand the causes of things - and propose solutions that have the power to transform the world we live in.

A member of the Russell Group, the University of Sheffield has a reputation for world-class teaching and research excellence across a wide range of disciplines. The University of Sheffield has been named University of the Year in the Times Higher Education Awards 2011 for its exceptional performance in research, teaching, access and business performance. In addition, the University has won four Queen's Anniversary Prizes (1998, 2000, 2002, 2007), recognising the outstanding contribution by universities and colleges to the United Kingdom's intellectual, economic, cultural and social life.

One of the markers of a leading university is the quality of its alumni and Sheffield boasts five Nobel Prize winners among former staff and students. Its alumni have gone on to hold positions of great responsibility and influence all over the world, making significant contributions in their chosen fields.

Research partners and clients include Boeing, Rolls-Royce, Unilever, Boots, AstraZeneca, GSK, Siemens, Yorkshire Water and many more household names, as well as UK and overseas government agencies and charitable foundations.

The University has well-established partnerships with a number of universities and major corporations, both in the UK and abroad. The White Rose University Consortium (White Rose) is a strategic partnership between 3 of the UK's leading research universities of Leeds, Sheffield and York. Since its creation in 1997 White Rose has secured more than £100M into the Universities.

Over the past century, the Medical Research Council has been at the forefront of scientific discovery to improve human health. Founded in 1913 to tackle tuberculosis, the MRC now invests taxpayers' money in some of the best medical research in the world across every area of health.

Twenty-nine MRC-funded researchers have won Nobel prizes in a wide range of disciplines, and MRC scientists have been behind such diverse discoveries as vitamins, the structure of DNA and the link between smoking and cancer, as well as achievements such as pioneering the use of randomised controlled trials, the invention of MRI scanning, and the development of a group of antibodies used in the making of some of the most successful drugs ever developed.

Today, MRC-funded scientists tackle some of the greatest health problems facing humanity in the 21st century, from the rising tide of chronic diseases associated with ageing to the threats posed by rapidly mutating micro-organisms. http://www.mrc.ac.uk

The MRC Centenary Timeline chronicles 100 years of life-changing discoveries and shows how our research has had a lasting influence on healthcare and wellbeing in the UK and globally, right up to the present day. http://www.centenary.mrc.ac.uk

The Wellcome Trust Sanger Institute is one of the world's leading genome centres. Through its ability to conduct research at scale, it is able to engage in bold and long-term exploratory projects that are designed to influence and empower medical science globally. Institute research findings, generated through its own research programmes and through its leading role in international consortia, are being used to develop new diagnostics and treatments for human disease. http://www.sanger.ac.uk

The Wellcome Trust is a global charitable foundation dedicated to achieving extraordinary improvements in human and animal health. We support the brightest minds in biomedical research and the medical humanities. Our breadth of support includes public engagement, education and the application of research to improve health. We are independent of both political and commercial interests. http://www.wellcome.ac.uk

Contact details Don Powell Media Manager
Wellcome Trust Sanger Institute
Hinxton, Cambridge, CB10 1SA, UK
Tel +44 (0)1223 496 928
Mobile +44 (0)7753 7753 97
Email press.office@sanger.ac.uk End of Notes to Editors


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[Press-News.org] Fishing for solutions
Examining function of all genes in the zebrafish genome to benefit human health