Sophisticated Genome Biology in the Tiny Fruit Fly

The fruit fly Drosophila has long been one of the workhorses of genetics and developmental biology. But for many genomic studies, fruit flies have had one big disadvantage: their small size.

As sequencing has become more sophisticated, experiments that were not possible in the fly just a few years ago, such as analyzing gene expression changes in a few cells, are now quite possible, says Don Fox, an Assistant Professor in the Department of Pharmacology and Cancer Biology.

Fox is taking advantage of that new potential to investigate two separate but partially overlapping areas of study. First of all, he wants to know which genes spring into action when tissues get injured and how that changes as flies advance into old age. Second, his lab is preoccupied with cells in the fly gut that are particularly prone to duplicating their genomes, forming genomically unstable polyploid cells similar to those that turn up in many human cancers. Fox wants to know exactly what it is that makes those cells unstable.

He is using sequencing approaches both to characterizethosepolyploidgenomesandto explore gene expression changes over time, with data generated in the IGSPs Genome Sequencing & Analysis Core Resource. Fortunately for Fox who arrived at Duke a year ago well-versed in genetics and cell biology and just beginning to tackle questions on a genomic scale his new lab is positioned right across the hallway from his colleague and long-time IGSP member Dave MacAlpine.

MacAlpine and his team are experts in genome biology,havingplayed animportantrolein modENCODE, an effort to classify all of the regulatory elements in the fly genome. The MacAlpine and Fox labs meet weekly in what is a mutually beneficial collaborative arrangement; Fox gains support in genomics and bioinformatics while MacAlpine gainssupportinmovingfromapproachesin Drosophila cell lines to those in whole fruit flies.

Its allowed my lab to be kind of fearless, Fox says. We can take on these bioinformatics-heavy experiments, which can easily be overwhelming. When I was contemplating where to start a lab, that opportunity for collaboration at Duke was a huge selling point.

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Sophisticated Genome Biology in the Tiny Fruit Fly