Identification of regulatory regions associated with regeneration in Annelids

 Stage · Stage M1  · 2 mois    Bac+4   Institut Jacques Monod - Stem Cells, Development and Evolution Team · Paris (France)

 Date de prise de poste : 10 avril 2023

Mots-Clés

Regeneration Comparative genomics Gene regulation Annelids

Description

Scientific background:

Regeneration, the ability to restore lost body parts, is a widespread phenomenon in animals. Whilst this ability is somehow limited in classical developmental model organisms, a variety of animals belonging to every main branch of metazoans are able to regenerate complex structures upon injury, such as limbs or even their whole body from a small piece of tissue in some cases. In the lab, we use the annelid Platynereis dumerilii, an emerging developmental biology model to study regeneration. After amputation of the posterior part of their body, Platynereis worms are able to regenerate both the pygidium (the posteriormost differentiated part of the body, which bears the anus) and a subterminal growth zone through the formation of a regeneration blastema (mass of undifferentiated proliferating cells that accumulate at the damaged surface underneath the wound epithelium).

This regeneration process involved the expression of a number of genes with precise and specific timing and localization. The expression of these genes is regulated by regions called enhancers, which are located around target genes. In animal genomes, such regions can be identified by scanning genome-wide multiple alignments to find non-coding regions conserved between a wide number of species, like ultra-conserved regions which function as developmental enhancers. Such comparative methods have been recently used to identify a wide number of enhancers in animal genomes.

Internship goals & missions

The main goal of the M1 internship project is the identification and analysis of regulatory regions involved in regeneration in the Platynereis dumerilii genome using an in-silico approach. Using genome-wide multiple alignments of >20 annelid genomes and available comparative methods, the student will identify conserved regions in the Platynereis dumerilii genome, identify which genes these regions regulate and whether these genes are linked with regeneration program identified in Platynereis from RNA-seq data generated in the lab, or identified in other species using publicly available RNA-seq data. The student will also study how these regions evolve (e.g. ultra-conservation or lineage-specific accelerated evolution) and how these patterns of evolution are linked with the regenerative capabilities of the species. During this project, the student will develop and enhance his/her skills in basic script (bash), data analysis (python, R), statistics (R) and High-Performance Cluster usage. He/she will use programs and pipelines available and widely used by the community, and write his/her own programs based on the necessities of the project.

References related to the internship:

Bideau, L., Kerner, P., Hui, J., Vervoort, M. & Gazave, E. Animal regeneration in the era of transcriptomics. Cell Mol Life Sci 78, 3941–3956 (2021).

Clément, Y., Torbey, P., Gilardi-Hebenstreit, P. & Crollius, H. R. Enhancer–gene maps in the human and zebrafish genomes using evolutionary linkage conservation. Nucleic Acids Res 48, 2357–2371 (2020).

Visel, A. et al. Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat. Genet. 40, 158–160 (2008).

Hubisz, M. J., Pollard, K. S. & Siepel, A. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief. Bioinformatics 12, 41–51 (2011).

Candidature

Procédure : To apply, please send a mail to Yves Clément describing your background and interest for this internship. Please include an up-to-date CV, grades report for the previous year, and, if you have done a previous internship, contact information of your supervisor.

Date limite : None

Contacts

Yves Clément

 yvNOSPAMes.clement@ijm.fr

Offre publiée le 18 novembre 2022, affichage jusqu'au 16 mars 2023