Mots-Clés

alpha satellite DNA centromeres long read DNA sequencing genome annotation sequence classification Primates

Description

The centromeres of eukaryotic chromosomes are made up of tandemly repeated DNA sequences, also known as satellite DNA. Thousands of copies of monomers are found next to each other in a head to tail configuration. Those sequences may participate in centromere function but also in heterochromatin assembly and gene regulation mechanisms. The best studied satellite DNA, which represents up to 5% of the human genome, is called alpha satellite DNA and has a monomer length of 171/172 bp. Several subfamilies of diverged monomers can be distinguished that differ in their distribution along chromosomes and often display multimeric periodicities. Satellite DNA has been shown to vary between even closely related species but the centromeres of all "higher" primates (i.e. Catarrhini and Platyrrhini) are based on alpha satellite DNA sequences and some subfamilies are shared between related species.

The mechanisms that sustain the evolution of satellite DNA are not completely understood but recombinational processes are believed to be responsible for the recurrent emergence of new satellite DNA arrays (Smith 1976). Our team has started to address the evolution of alpha satellite DNA by focusing on a clade of Catarrhini (a subgroup of Primates including great apes) for which numerous species are available (Cacheux et al 2016, Cacheux et al 2018). We have also developed specific bioinformatic approaches for the classification of alpha satellite DNA (Haschka et al 2020). Additional tools have recently become available for the detection and annotation of satellite DNA (Wlodzimierz et al 2023). The recent explosion of genome sequencing projects as well as the advent of long-read sequencing methods has provided a wealth of new experimental datasets for exploring the diversity of satellite DNA across primate species. In particular, several Strepsirrhini (another subgroup of Primates) genomes have become available but have been poorly explored so far (Shao et al, 2023).

In this context, the main objectives of the internship will be to :
1) characterize satellite DNA in a few Sterpsirrhini species.
2) identify conserved features between satellite DNA from Strepsirrhini and alpha satellite DNA.

The outputs of this project will be new analytical tools for the study of satellite DNA as well as new insights into the evolutionary mechanisms of those sequences.