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RNA Biology & Applied Bioinformatics

Group leader dr Timo Breit

In recent years RNA has increasingly gained attention of life sciences researchers as a key regulator of molecular processes in living organisms. This renewed interest was mainly sparked by the discovery of miRNA and other important non-coding RNAs, as well as the development of transcriptomics technologies such as microarray technology and next-generation sequencing.

The importance of RNA is underlined by the fact that it is estimated that over 70% of the human genome is transcribed into RNA, while less than 2% of the total genomic sequences encode the ~25,000 protein-coding genes. This is evidence for a major role of RNA in many cellular processes, such as gene-expression regulation, epigenetic regulation, splicing, signal transduction, molecular transport and localization.

To gain insight in the regulatory roles of RNA, our research focusses on the characterisation of maternal RNAs and cell-free RNAs combined with research to the dynamics of these transcriptome components. As we have our own next-generation system (Ion Proton), we will also try to discover new types of RNA.

This kind of research demands the use of advanced omics technologies and associated bioinformatics. Since omics bioinformatics are still immature, we also do applied bioinformatics research on how to optimally design an omics experiment, analyse the data, and interpret the results.

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The MAD: Dutch Genomics Service & Support Provider is the genomics and transcriptomics expertise center of the University of Amsterdam. We perform omics (microarray & next-generation sequencing) technology research as well as operate as worldwide transcriptomics service provider and support partner for academic and industrial R&D projects. We have one next-generation sequencing technology platform (Ion Proton) and two microarray technology platforms (Agilent and Affymetrix).

The MAD was founded in 1999 with funding from the Dutch government plus major investments from several industrial food and pharma partners. The aim was to establish a proficient transcriptomics facility for life-science researchers from both within and outside the UvA. The projected tasks of the facility would encompass the execution of transcriptomics experiments as well as the analysis of the results. The laboratory was officially opened for external services at April 5, 2001. The tasks of the expertise center encompassed the design, production and use of (custom-made) microarrays, as well as analysis of the experimental results. Recently, next-generation sequencing services are added. Nowadays, the MAD consists of a "Wet-Lab" for molecular-biology analyses service and support, and a "Dry-Lab" for bioinformatics service and support.

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Over the years, both RB&AB research group and the associated MAD have expanded and are working at the frontier of genome-wide molecular-biology technology, research and data analysis. The multidisciplinary approach of a mix of biological research, genomics & bioinformatics expertise, plus support, proved to be a successful concept. The close collaboration of the RB&AB research group with the MAD Dry- & Wet-labs, and biologists creates a stimulating environment that is beneficial for all clients and partners, today and in the future.