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Research Projects
RNA editing  |   Somatic Activity of Retrotransposons in Human  |   DNA editing of mammalian genomes  |   Alternative Splicing
Somatic Activity of Retrotransposons in Human

The retrotransposition cycle
Retrotransposons’ activity can cause dramatic changes in the human’s genome. Therefore, exploring their activity and its influence arouses great interest. Retrotransposons are genomic sequences that duplicate in a “copy-paste” mechanism through an RNA intermediate followed by reverse transcription and insertion into a new genomic location.

Insertion events in protein-coding or regulatory regions can alter genome function, contribute to genetic innovation and impacts the evolution of primate genomes in terms of both structure and function.

L1, Alu and SVA retrotransposons, who collectively account for approximately one-third of the human genome, are the only transposable elements currently known to be active in humans. The large-scale studies of retrotransposon are now possible due to huge development in next generation sequencing. This research area is relatively new and of great interest, due to the fact that retrotransposons continue to produce genetic diversity in humans, and also cause diseases as a result of their integration into genes. In this research, we study the somatic activity of retrotransposons in the human genome using next generation sequencing data. We focus mainly on characterizing retrotransposons in the human genome, identifying recent events of insertion and comparing the expression levels of retrotransposons in various tissues.

Research description : Identification of DNA editing sites. APOBEC3 mammalian proteins are able to induce C-to-U mutations in retrotransposons during reverse transcription. This led to numerous apparent G-to-A mutations between extant retrotransposon copies that might have dramatically affected their evolution. We are working on computational identification and characterization of those sites in various genomes and are examining intra- and inter-genomic diversity of DNA editing rates and patterns.