Repeats, in particular transposable elements (TEs), are major components of eukaryotic genomes given their impact on genome evolution and species adaptation. TEs are mobile repeated sequences, which can make up very large proportions like about 50% of mammalian genomes to more than 80% in the genomes of some plants. They can promote various types of mutations, from gene interruption and expression alteration to large scaled chromosomal rearrangements, but can also promote the formation of new genes. Despite their deleterious effects, TEs are currently considered as major actor in genome evolution due the genetic and epigenetic diversity they can generate.
Even if they have a fundamental biological role, detection and analysis of TE sequences are still technologically challenging. The current era of high throughput sequencing offers numerous opportunities to analyze them at different scales. However, the length and quality of sequenced reads make their detection and annotation difficult (40% detection error). Moreover, the presence of TEs in a genome can also lead to important assembly errors due to rearrangement errors and the merge of repeats, and to complicate the identification of splicing events and the estimation of gene expression in transcriptomic analyses. It is thus important to be able to identify these sequences in genomic and transcriptomic data.
Since several years, a large number of bioinformatic tools have been developed allowing a better identification of TEs in genomes. New tools are released regularly to follow the progress of sequencing technologies but also to answer particular biological questions allowing to go from the TE annotation in assembled or unassembled genomes, to insertion polymorphism detection in natural populations. The result is a particularly large choice for users leading to difficulties in thedetermination of the best tool(s) to use according to the case.
Thus, by gathering together actors from the bioinformatic field specialized in TE analyses as instructors, this CNRS school aims at proposing a direct access to this knowledge to help handling and using bioinformatic tools for the detection and analysis of TEs in genomic and transcriptomicdata.
This school is sponsored by the CNRS, the IDEXLyon, the GDR BIM and the FR BioEnviS.
GOALS
This CNRS school aims to form users to the best bioinformatic techniques allowing the identification and the analysis of TEs in sequencing data. The chosen format will give the opportunity for strong interactions between instructors and trainees during a whole week, facilitating the learning but also with time for informal discussions allowing the establishment of collaborations.
The public concerned are researchers and engineers daily involved in the analysis of sequencing data, as well as researchers, PhD students and post-doctoral fellows wishing to broaden their research subject in this area.
The prerequisite is mainly to know genomics. It is not necessary to know the biology of the repeated sequences. The practical instruction will be performed on computers and the participants must have already practiced the use of Unix-type command lines.
Limited to 30 persons.
CONTACT
Emmanuelle Lerat
Laboratoire Biometrie et Biologie Evolutive
Universite Claude Bernard - Lyon 1
UMR 5558 - Bat. Mendel
43 bd du 11 novembre 1918
69622 Villeurbanne cedex France
emmanuelle.lerat@univ-lyon1.fr
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