Indiana University’s Bloomington Drosophila Stock Center, a clearinghouse for genetically defined lines of fruit flies that serves scientists in 2,600 laboratories worldwide, has reached a milestone with completion of the most comprehensive set of chromosome deletions for any multicellular organism on earth.
Scientists studying the fruit fly (Drosophila melanogaster) use chromosomes with deleted stretches of DNA to map harmful mutations to extremely small groups of side-by-side genes.
“The best way to discover the function of a gene is to break it and then find out what goes wrong,” said IU research scientist Kevin Cook, senior author on a recent paper in Genome Biology that announced the achievement. “If you have a mutation that causes a disease or defect in the fly when both chromosomes carry the mutation, you can identify the broken gene by making an abnormal fly with the mutation and a deletion. The mutated gene must be one missing from the deletion chromosome. Since we know exactly which stretch of DNA is missing in every deletion, we can map mutations with exquisite resolution just by breeding flies.”
Human and fly cells work in fundamentally the same ways, and almost three-fourths of all known human disease genes have a match in the Drosophila genome. Just like us, fruit flies can have heart problems from a high-fat diet, develop insulin resistance on high-sugar diets and respond to pharmaceuticals. Drosophila melanogaster is currently being used to study a broad range of biological processes shared with humans — including metabolism, development, physiology and aging — and research on the fly counterparts of human disease genes is providing insights into the molecular mechanisms of disorders like Alzheimer’s, Huntington’s, Lou Gehrig’s and Parkinson’s diseases and cancer, diabetes and epilepsy.
“There are experimental genetic approaches in flies that simply aren’t available in mammalian research, so it’s easier to make progress,” said co-author Thom Kaufman, a Distinguished Professor in the IU Bloomington College of Arts and Sciences’ Department of Biology. “And the techniques and resources available to fly geneticists are much more sophisticated and easier to use.”
The deletion strains allow mutations to be mapped to small chromosome regions of a median of only nine genes.
“Once a scientist gets a mutation mapped this closely, they can usually identify the most likely candidate gene based on its DNA sequence characteristics,” Cook said.
In many cases, deletions alone can be used to map a mutation to a single gene. Altogether, the new deletions cover a remarkable 98.4 percent of the fly genome, more than any other multicellular organism. Covering 100 percent would mean deleting genes that the fly needs in two copies for viability and fertility, yet deletion coverage was maximized by getting as close to those “haplolethal” and “haplosterile” genes as possible.
“In the process,” Cook said, “we put together the most complete catalog of these special genes in any plant or animal.”
In addition to mapping mutations, deletions are used by researchers to judge just how badly particular mutations harm genes and to identify genes that work together in cellular pathways. They are often used in screening for new mutations.
“Knocking out genes on purpose is the primary way geneticists figure out the connection between DNA sequence and biological function,” Cook said. “Deletions have so many important experimental applications they are used in almost every Drosophila research project.”
Half of the 1,600 molecularly defined deletions were generated at IU under a 12-year, $2.5 million dollar grant from the National Institutes of Health. The remaining deletions were generated by the European Union-sponsored DrosDel consortium and by Exelixis Inc. All the deletions were made using a technology that employs special DNA cutting sites carried on transposable genetic elements inserted throughout the genome.
The rapidly expanding Bloomington Drosophila Stock Center accepted its first strain in 1987 and currently maintains 40,000 different genetically characterized lines. Researchers from around the world ordered 215,000 living Drosophila samples in 2011 alone, with deletions being the highest in demand. The center has 42 employees and is funded both by user fees and grants from the National Science Foundation, the National Center for Research Resources, the National Institute of General Medical Sciences and the National Institute of Child Health and Human Development.