News Release

Switching on the fly genome

Peer-Reviewed Publication

European Molecular Biology Laboratory

For the first time, scientists at the European Molecular Biology Laboratory (EMBL) have used a new technique to monitor the activity of the complete genome of the fruitfly, one of biology’s most important model organisms. The method, called SAGE, allowed them to watch what happens as cells receive a signal that helps form tissues. They discovered that hundreds of fly genes respond when cells are stimulated with a molecular signal called JNK. Their work is reported in this month’s issue of Developmental Cell.

While SAGE has already been used to study human and mouse cells, researchers regard its adaptation to the fruitfly as a critical step. “A SAGE study creates a lot of hypotheses about genes that may be involved in specific biological processes,” says Dirk Bohmann, whose group headed the project. “You want to test those hypotheses in a whole organism – one that we know a lot about, which has a short lifespan, and on which it is ethically acceptable to perform experiments. The fruitfly has been used in genetic studies for nearly a century, so we have powerful tools to investigate it that don’t exist in other organisms.”

Molecular signals have their effects by switching on and off genes; an activated gene produces RNA molecules. SAGE can collect and count them all, directly showing how active each gene is. Heinrich Jasper and other members of the Bohmann group showed that activating the JNK signal increased the output of over 300 genes and decreased that of over 300 others. “Many of these had never been connected to JNK signaling before,” Bohmann says. “Our follow-up experiments quickly eliminated red herrings and gave us a good idea of the genes likely to guide similar processes in mice and other animals.” Researchers knew that the JNK signal helped the skin to form properly, but they didn’t know how. One gene in particular, called profilin, revealed a a very clear link between the signal and major structural rearrangements within cells that permit them to bind with each other and form tissues.

Researchers hope that SAGE can be used to generate profiles of disease cells, creating new diagnostic tools and identify potential targets for drugs and therapies. This work will depend heavily on predictions developed in animal systems such as the fruitfly.

For a simple explanation of how SAGE works, and links to related topics, see the page on our website: http://www.embl.org/info/sage
Check out the genome of the fruitfly, Drosophila, at: http://www.flybase.org
And for a direct look at the human genome, go to: http://www.ensembl.org
A new method opens up the genome of one of biology’s most important model organisms

FULL VERSION

Completely sequencing the genomes of human and other organisms is so important because it will greatly speed up our understanding of how genes influence the lives of cells and animals. Genes direct the process by which a mature organism develops from a single cell, how it responds to the environment, and what happens in a disease. Researchers know that hundreds of genes might be involved in any given biological process, but in the past they could only study a small number of them at a time. Today, powerful new technologies are being developed that can monitor the activity of thousands of genes, even a whole genome. Now Henri Jasper, Dirk Bohmann, Vladimir Benes and their colleagues at the European Molecular Biology (EMBL) in Heidelberg have gotten one of these methods up and running in one of biology’s most important model organisms, the fruitfly. Their work is reported in the October issue of Developmental Cell.

The approach, called SAGE (for Serial Analysis of Gene Expression), has existed for a few years and has been used successfully to study human and mouse cells. Getting it to work in the fruitfly is a critical step, Bohmann says, because it will allow researchers to understand the effects of multiple genes on a whole animal. “For this you need an organism with a rapid lifecycle, and one that has been thoroughly studied – scientists have been researching fly genetics for almost a century.”

Molecular signals switch genes on and off, causing the cell to produce new molecules, changing its shape and behavior. An event may require hundreds of switches to be thrown, and understanding basic biological processes will require seeing the whole pattern. But flies have about 15,000 genes (humans have at least twice that many), and until recently, it has been impossible to watch more than just a few at a time. SAGE and another new technology, called DNA chips, are rapidly breaking down the barrier. By identifying and counting RNA molecules, which are produced when genes are switched on, they can potentially monitor the entire genome.

In the current study (reported in Developmental Cell), Bohmann and his team discovered that over sixty genes responded dramatically to a particular developmental signal, and over 500 more responded mildly to it. Identifying the genes enabled them to perform experiments to uncover how these genetic programs function in the fly.

For years the team has been studying a particular type of molecular “signal relay” called JNK. In flies, this signal helps sheets of skin cells grow towards each other and knit together. This fuses the skin over the back of the embryo, like closing a zipper. If anything interrupts the JNK signal at critical moments in the process, there will be a gaping hole. “There are very strong parallels between this and some developmental processes in humans and other animals,” says Heinrich Jasper, who led the recent project in Bohmann’s lab. “What we are learning about flies may give us a good model to study medically-important questions.”

Jasper and his colleagues used two special, radically different types of fly embryos in the experiments. In one type, the JNK information route is switched off, and the signals don’t reach the genes. In the other, JNK is overactive, sending a signal of abnormally high intensity. By contrasting these two exaggerated situations, they hoped to get a clear view of the pattern that the signal evokes.

Vladimir Benes and other members of Wilhelm Ansorge’s group helped adapt SAGE to the fly, and Christian Schwager played a key role in analyzing the results by computer. Intriguingly, some of the genes they found had never been directly connected to JNK signaling before.

An investigation of these genes revealed a clear link between JNK and architectural molecules that form fibers within the cell, giving it a particular shape and the ability to bind to its neighbors. These fibers, made of a molecule called actin, push at the forward edges of cells and make them extend towards sheets of skin at the opposite side of the fly’s back and thorax – closing the gap over the back is an important function of the JNK signal. Jasper and Bohmann found that JNK activation switches on a gene called profilin, leading to an increased concentration of the profilin protein. This molecule directly influences the formation of actin fibers.

Human and mammalian cells use signals that closely resemble JNK in flies; the study suggests that the signal may help wounds to heal. “Some of these are genes that get activated when cells are placed under stress – for example, when there has been an injury,” Jasper says.

Perhaps most importantly, this is a flagship study for the SAGE method. “What does it mean for an organism as a whole if the activity of genes x, y, and z suddenly goes up or down?” Bohmann says. “We can make hypotheses, but they need to be tested, and this is harder to do in mice or people than in flies. Because the lifecycle of the fly is so short, this method let us identify and test critical genes – and eliminate the red herrings – in a matter of weeks. Additionally, the long tradition of fly studies has given us powerful investigative tools that we don’t yet have in other organisms. Solid results in the fly show us where to look for parallel processes in mice and humans that might have a medical relevance.”

One hope is that SAGE will help create profiles of diseases. In cancers and infections, cells undergo significant changes in patterns of gene activity. By counting RNAs, SAGE should be able to pinpoint significant differences between healthy and diseased cells. This will not only create diagnostic tools – it will give researchers strong clues about where to aim drugs and how to develop therapies. The proving ground for such hypotheses will have to be model systems such as the fruitfly.

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