The Mobile Genome in Human Evolution

PI: Alessio Boattini
Large part of the human genome (~66-69%) is made by repetitive elements, most of which are trasposons (~46%). Trasposons are mobile elements that can shift their position or produce copies of themselves via copy-and-paste or cut-and-paste mechanisms. Traditionally, transposable elements were dismissed as genomic “parasites” or “junk DNA”. However, recent studies demonstrated that trasposons had a key role in the evolution of innovations such as the placenta in Mammals and the adaptive immune system in Vertebrates. In our species, they contribute to processes such as embryogenesis and neurogenesis. The aim of our researches is to explore and understand the role of transposable elements in the recent evolution of Homo, as well as their functional and biomedical implications.
Our group is currently pursuing the following projects:
1) Comparisons with ancient genomes and chimp/bonobo. In order to evaluate the impact of transposable elements in the recent evolution of our species, we compare our insertion patterns with those of extinct hominins (Denisova, Neanderthal) and of our closest relatives (bonobo, chimp), thus identifying and characterizing species-specific insertions. From a methodologic point of view, we are developing bio-informatic tools for the identification of insertions in ancient genomes.
2) Variability of insertions in modern genomes. Transposable elements, thanks to their absence/presence polymorphisms, are an ideal tool for phylogenetic research. Consequently, the identification of their variability patterns in modern human populations is an effective mean to re-construct our recent genomic history and to identify potential selection events related to transposon insertions.
3) Long reads sequencing. Modern Next-Generation Sequencing (NGS) techniques yield short sequences (reads). This fact makes the identification of transposable elements insertions quite a difficult task. Furthermore, since NGS sequences are typically aligned on the reference genome, structural variants cannot be observed. For these reasons, we are performing experiments with new sequencing techniques (Oxford Nanopore) that yield much longer reads (~10000bp), with the aim of drafting a first repertoire of genomic structural variants.