New gene-editing system enables large-scale studies of gene function.
CAMBRIDGE, Mass.--In a big step toward identifying a "genetic construction kit" for animal development, MIT researchers report in the May 13 online advance issue of Nature Genetics that they have identified 75 genes required to create a baby zebrafish. The researchers' quest is to identify a large proportion of the 2,400 necessary genes.
This is the first time anyone has reported in one fell swoop such a large number of genes required for the embryonic development of a vertebrate.
The zebrafish is a model for animal and human development and disease. Nancy Hopkins, Amgen professor of biology at MIT, says each of the 75 genes identified in the study has at least some similarity with a known human gene, and a few are known to be involved in human diseases such as diabetes and cancer.
If scientists knew that mutations of a certain gene were linked to a specific condition or disease, they could potentially target drugs to affect those genes or screen individuals for genetic susceptibility to diseases.
"About one and a half years from now, we will have cloned about 500 genes of this type," Hopkins said. "People have estimated that around 2,400 genes are essential for embryonic fish development. Thus, we will isolate about 20 percent of the total."
In addition to Hopkins, authors include lab members Gregory Golling, Adam Amsterdam, Zhaoxia Sun, Marcelo Antonelli, Ernesto Maldonato, Wenbaio Chen, Shawn Burgess, Maryann Haldi, Sarah Farrington, Shuh-Yow Lin and Robert M. Nissen, as well as Karen Artzt of the University of Texas at Austin.
A FAST APPROACH
The approach developed by Hopkins and colleagues is to infect thousands of early zebrafish embryos with a virus that randomly disrupts genes. In this way, they are able to clone the genes very quickly because the virus acts as a molecular tag in the genome. "It seems that once a week or so, we come up with new genes (to look at) and that's very exciting," said Amsterdam, senior postdoctoral associate in MIT's Center for Cancer Research. "This is a fast route to new knowledge."
Other zebrafish laboratories working on "forward genetics," or isolating genetic function without working backward by observing the effect of knocking out selected genes, collectively have identified around 50 genes in more than five years, averaging two to four years per gene.
"For us, it is only two to four weeks per gene because of the method for making mutations that we developed," Hopkins said. "The idea that you could do forward genetics in vertebrate animals at this rate is amazing."
Hopkins describes the overall goals of genetics today as a three-step process: mapping the genome of humans and other living things, uncovering the function of individual groups of genes and determining exactly how genes do their jobs. Her goal falls into the second category--assigning probable functions to some of the genes--and the third--understanding how the genes do their respective jobs.
Although the zebrafish has approximately 30,000 to 50,000 genes, only a small proportion of them is necessary for normal development. Hopkins surmises that there is some minimum number of genes needed to create a "basic" model of an animal, with significantly more needed for a more robust organism that can survive a variety of adverse conditions.
As Hopkins' lab continues to uncover genes which, when mutated, lead to fatal flaws in the organism, Amsterdam finds he is most intrigued by the ones that seem to come from left field.
"Some genes make sense (in terms of conditions or diseases) and others are not so obvious," he said. Amsterdam suspects that it will be this "novel class" of genes-ones that have no known function in the zebrafish or in humans that may generate the biggest payoff in terms of future cures by pointing researchers toward parts of the genome that they may not otherwise have rushed to explore.
This work is funded by the National Institutes of Health and Amgen.