The BioSapiens project: Unravelling the secrets of the human genome

When the human genome was sequenced in 2003, it was rightly hailed as a major breakthrough. However, for many scientists, obtaining the three billion letter sequence of our DNA was just the
first step of a much greater challenge, namely understanding how our genome works.

This task is known as genome annotation, and it involves determining the function of every stretch of DNA. This is detailed work. For example, it is not enough to simply say that a sequence
codes for a protein; the structure and function of the protein also need to be investigated in depth.

All of this work leads to the generation of vast amounts of different kinds of data which needs to be managed and analysed in a systematic, coherent fashion, and this is where bioinformatics
comes in. Bioinformatics researchers specialise in the development of methods for the storage, retrieval and analysis of data ranging from protein structures and experimental results to patient
statistics. To do this they draw on techniques and concepts from a variety of disciplines, including mathematics, biochemistry, genetics, physics and linguistics.

In Europe, the top people in the field are gathered together in a Network of Excellence called BioSapiens, which is funded under the Sixth Framework Programme’s ‘Life sciences, genomics and
biotechnology for health’ thematic area.

One of the primary achievements of the project so far has been the development of new bioinformatics tools and their integration into existing biological data management systems.

These tools were tested and validated by scientists around the world in the framework of the international ENCODE (Encyclopedia of DNA Elements) project, which was launched in 2003 by the
National Institutes of Health in the US. The initial goal of ENCODE was to determine the function of 1% of the genome.

The results of this pilot phase were published earlier this year, and they challenged the established idea that the genome consists of a small number of genes surrounded by large regions of
inactive, ‘junk’ DNA. Instead, the study revealed that most of the DNA in our cells is active in some way, with many of the regions of our genome which were formerly dismissed as junk turning
out to have regulatory functions. These regulatory sequences are responsible for telling our genes when and where to be active. This has important implications for health researchers, as many
diseases are caused by mutations in regulatory sequences.

‘Our results reveal important principles about the organisation of functional elements in the human genome, providing new perspectives on everything from DNA transcription to mammalian
evolution,’ commented BioSapiens project partner Ewan Birney of the European Molecular Biology Laboratory, who led the data analysis work. ‘In particular, we gained significant insight into DNA
sequences that do not encode proteins, which we knew very little about before.’

The BioSapiens project still has another year to run, and during that time the researchers plan to fine-tune their tools for the next stage of the ENCODE project, which involves annotating the
remaining 99% of the human genome.

However, the BioSapiens project is not restricted to research activities; it also has an educational component.

‘There is a real need for training in bioinformatics,’ explained Professor Alfonso Valencia of the Spanish National Cancer Research Centre and BioSapiens’ Outreach Coordinator. There is already
a waiting list for the courses, which introduce participants to the basic concepts of bioinformatics and train them on how to use the tools available in their own research.

The European Commission speaks very highly of the BioSapiens project. The project officer at the European Commission, Dr Frederick Marcus, told CORDIS News it is ‘one of my best projects’ and
described its leaders as ‘superstars’. According to Dr Marcus, the project’s success can be put down to the fact that the partners work extremely well together.

Professor Valencia confirms this analysis, noting that the project has involved far more truly collaborative work than any of the other projects he has been involved in.

Meanwhile Dr Marcus is clear about the ongoing importance of bioinformatics research, which will remain a hot topic for the Commission under the Seventh Framework Programme (FP7).
‘Bioinformatics is an absolutely essential part of health research,’ he told CORDIS News.

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