Transposable elements in bacterial and eukaryotic genomes
Transposable elements (TEs) are repeated sequences present in all eukaryotic genomes and almost prokaryotic genomes. TEs can copy themselves inside the cell of the host genome, from a mechanism different of recombination and called the transposition. With the ability to multiply into genomes, TEs can correspond to a large percentage of somes eucaryotic genomes : from few percents (dozen) in Arabidopsis thaliana or Drosophila melanogaster ; they can represent more than the half of host genome such as mouse (60%), human (70%) or wheat (80%); and in some cases only one family (i.e. Alu in human) can have millions of copies in one host genome. If the host genome has created during evolution some mechanisms to regulate or generally avoid the TE transposition (TE insertions can create harmful mutations): heterochromatin, and ncRNAs (such as siRNAs or piRNAs). TEs are one of the biggest molecular mechanism of genome evolution. For example, about 10% and 50% of spontaneous mutant phenotypes in mouse and fly genome respectively and are caused by de novo TE insertions within the coding or noncoding portion of genes.
Transposable elements are classified based on its sequence features such as palindrome, repeat, motifs, its transposition proteins and the transposition mechanism itself. An active TE (i.e TE that contains transposition proteins) like any gene, possess with the transposon genes all necessary regulatory motifs necessary for its transcription and regulation but within its own sequence : promoters, splice sites, termination sites, and enhancers/insulators. On the contrary, an inactive TE losses the capability to transpose itself after mutations and/or deletions, but they represent the majority of TE in mammals genomes and are often called fossil TE. TE insertion/evolution also creates multiple positive roles for the host genome. For example, many TEs are inserted in introns and these insertions can create alternative splicing, polyadenylation sites (Figure), and regulating gene expression. They can also participate to the chromosome organization with the insulator CTCF motif within TE sequences. These mutations are specifically visible in developmental processes such as defects in oogenesis, disruption of homologous chromosome during meiosis, or activation of the unfolded protein response during differentiation of B lymphocytes.
In one of our projects, led by Sebastien Tempel, we are interested in the analysis of the evolution of transposable elements by detecting and comparing their internal patterns, espacially the regulatory gene motifs such as promoter sites and TFBS. Then we also study of the evolution of transposable elements and their relationship with their host genome : how they regulate the neighboring genes and how they reshape the genetic networks of some tissues.