Introduction

The facility was founded in 1999 when the Montpellier – Languedoc-Roussillon Genopole was set up. It is located on the Arnaud de Villeneuve campus, within the Functional Genomics Institute.

This platform offers the following services

• High-throughput sequencing
• Bio-statistics and bioinformatics

Applications available include de novo sequencing or re-sequencing of genomes, the study of the transcriptome of numerous animal, plant and prokaryotic species, but also techniques for studying chromatin structure and dynamics (ChIP-seq, 4C, Hi-C, etc.) and epigenetic modifications (DNA methylation). Genomic approaches on single cells are currently being developed.

The plateform is run by a team of 10 engineers: 6 molecular biologists and 4 bioinformaticians.

Equipments

Development objectives

The platform is currently working on methods to limit sequencing costs and reduce the biases linked to library construction methods, particularly in the context of transcriptomic studies.
It is also working on a method for evaluating the stability of the genome of cell lines (particularly iPS) during the various passages necessary for their growth.

Main achievements

• HRS-seq, a method to identify partitioned regions in nuclear bodies. Baudement MO et al. (2018) High-salt-recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies. Genome Res. 28:1733-46. doi: 10.1101/gr.237073.118.
• ISoLDE, a method for performing allelic RNA-seq. Reynès C et al. (2020) ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses. Bioinformatics. 36(2):504-13. doi: 10.1093/bioinformatics/btz564.

• Caubit X et al. (2016) TSHZ3 deletion causes an autism syndrome and defects in cortical projection neurons. Nat Genet. 48:1359-69. doi: 10.1038/ng.3681.
• Varrault A et al. (2017) Identification of Plagl1/Zac1 binding sites and target genes establishes its role in the regulation of extracellular matrix genes and the imprinted gene network. Nucleic Acids Res. 45:10466-80. doi: 10.1093/nar/gkx672.
• Morchikh M et al. (2017) HEXIM1 and NEAT1 Long Non-coding RNA Form a Multi-subunit Complex that Regulates DNA-Mediated Innate Immune Response. Mol Cell. 67:387-99.  10.1016/j.molcel.2017.06.020.
• Gautier M et al. (2018) The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird. Curr Biol. 28:3296-3302. doi: 10.1016/j.cub.2018.08.023.
• Du K et al. (2020) The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Nat Ecol Evol. 4:841-52. doi: 10.1038/s41559-020-1166-x.
• Puighermanal E et al. (2020) Functional and molecular heterogeneity of D2R neurons along dorsal ventral axis in the striatum. Nat Commun. 11:1957. doi: 10.1038/s41467-020-15716-9.
• Garot E et al. (2019) Plant population dynamics on oceanic islands during the Late Quaternary climate changes: genetic evidence from a tree species (Coffea mauritiana) in Reunion Island. New Phytol. 224:974-86 doi: 10.1111/nph.16052.
• JayP et al. (2021) Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms. Nat Genet. 53:288-93. doi: 10.1038/s41588-020-00771-1.
• Imarazene B et al. (2021) A supernumerary “B-sex” chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus. Curr Biol. S0960-9822(21)01134-9. doi: 10.1016/j.cub.2021.08.030.

Last update Nov 2021