Of small RNAs, gigabytes of sequences and the precious genome of the germline
May 15, 2015
Scattered throughout the genomes of plants, fungi, and animals are stretches of DNA called transposable elements, which can translocate from one genomic place to another. As these “jumping genes” often cause deleterious mutations, different genome protection mechanisms have evolved in all eukaryotes.
The central defence system in animals and humans is the piRNA pathway that is essential to suppress transposons in the cells of the germline. Without this pathway transposons are reactivated, which leads to severe damage of the germline genome and ultimately to sterility. The piRNA mechanism belongs to the group of small RNA pathways that are important gene regulatory systems that repress viruses, transposons, but also endogenous genes. The world of small RNAs was discovered via genetic studies in the early 1990s in plants and the roundworm Caenorhabditis elegans. Ever since, this is an area of intense research and it is now clear that nearly every biological process in eukaryotes is in some or the other way impacted by small RNAs.
An expert in this field is Julius Brennecke from the Institute of Molecular Biotechnology of the Austrian Academy of Sciences in Vienna. Together with his research group he was now able to reveal novel and exciting features of the piRNA pathway in the fruitfly Drosophila melanogaster, published in the journal Science today.
"The piRNA system utilizes small RNA snippets—the piRNAs—which fit like mirror images onto the transcripts of transposons and thereby initiate their specific destruction", says PhD student Dominik Handler, who is shared first author of the study together with Fabio Mohn, a postdoctoral fellow. How these small RNAs are produced is one of the big unresolved questions in the field. A key challenge for the cell is to make piRNAs only out of the right precursor RNAs, as processing of an inappropriate RNA might lead to the silencing of its own genes. "We discovered several patterns among piRNA populations, which allowed us to infer a novel piRNA biogenesis model and which revealed how the cell decides which precursor RNAs will be converted into small piRNAs", says Handler.
Brennecke emphasizes that this entire research would have been impossible without modern sequencing methods—generally referred to as "Next Generation Sequencing". In the last years, this new technology has evolved very quickly and has become much faster and cheaper. Ten years ago, one machine could sequence a maximum of 96 DNA fragments simultaneously; now hundreds of millions of fragments are possible. An impressive example of the groundbreaking nature of this technology is the sequencing of the human genome. This project lasted ten years, hundreds of scientists were involved, and the total costs were about three billion dollars. "Today we can sequence ten human genomes within a week for less than 1,000 dollars", says Andreas Sommer, head of the Next Generation Sequencing Unit at the Campus Science Support Facilities GmbH (CSF). This facility provides infrastructure and services for various research projects at the Vienna Biocenter. Almost all research groups on campus regularly use the services of the CSF, which allows a very efficient usage of its resources. However, the extremely rapid advancement of the technology is a big challenge. About every three years, considerable investments are necessary and the expenses for a new device are about 600,000 Euros.
"Next Generation Sequencing has revolutionized the understanding of pretty much every cellular process that deals with DNA or RNA", explains Sommer. His unit employs machines of the Illumina HiSeq series, which are among the most powerful devices on the market. After the sequencing process is finished, incredible amounts of raw data are produced: billions of As, Gs, Cs and Ts, the four basic letters of DNA. These then need to be analysed, a considerable challenge given the amount and complexity of the data. Indispensable for this are powerful computers and custom-made programs developed by PhD students or postdocs in research groups on campus.
The work of Julius Brennecke and colleagues shows how research nowadays benefits, but also relies on access to the highest possible technical equipment, a key competitive advantage of the Vienna Biocenter. This project is also a good example to show that research in biology nowadays takes place to a considerable amount of time at the computer. The picture of a biologist, who examines a bug under a microscope is certainly out-dated ", says Brennecke.