Constituent teams: Catherine ANDRÉ, Valérie DUPÉ, Marie-Dominique GALIBERT, Reynald GILLET, Luc PAILLARD, Gilles SALBERT
Keywords: DNA metabolism, genetics, epigenetics, cancer, rare diseases, translation.
Within chromatin, the genome carries both genetic and epigenetic information that drives the engagement of DNA-binding proteins as well as epigenetic readers. These in turn play major regulatory roles in the control of DNA replication, transcription, and repair. Genetic or hereditary diseases are often associated with genetic and/or epigenetic defects, which can be counteracted by various strategies.
Our teams use genetic and epigenetic approaches to analyse DNA metabolism, gene regulation in normal and pathological situations, at the level of cells and organisms. The SALBERT team runs genome-wide studies to understand the molecular basis of gene regulation and DNA replication. In addition, they use microscopy to investigate the dynamics of DNA repair proteins. The ANDRE and DUPE teams search for genetic or genomic alterations and for any gene networks tied to rare pathological diseases and cancers. One original aspect of the research led by Catherine ANDRE is the use of dogs naturally affected by illnesses to search in an alternative ethical way for new genetic alterations and therapies that can benefit both dogs and humans. The DUPE team does unique work on neurodevelopmental diseases, and they are closely linked with the hospital and clinical national reference centres (coordinated by members of that team). The GALIBERT team uses genetic approaches to deciphering molecular mechanisms that are associated with genetic alterations in cancers (melanoma and leukaemia), and aims at identifying drugs that modulate disease expressivity.
Genetic and epigenetic information mainly controls the gene expression program at the transcriptional level. Yet in eukaryotic cells, the post-transcriptonal steps of gene expression are there to shape the mature transcriptome, and therefore have a deep influence on the overall readout of the transcriptomic programs. For example, it is now known that alternative splicing shapes the majority of mature mRNAs, and that the exact nature of the expressed isoform is a critical determinant of the cellular differentiation state. These complex yet general regulations of gene expression are mainly controlled by interactions between regulatory RNA-binding proteins (RBPs) or miRNAs and RNA molecules. The PAILLARD team studies the impact of RBPs on the differentiation of epithelial cells by analysing both their RNA targets and the consequences of RBP depletion both the molecular and organismal levels. After these interactions, the genetic information is decoded into proteins by the cell’s translational machinery. The GILLET team unravels this process of translation at the molecular level, thanks to cryo-EM structural analysis. They also study the quality-control processes of ribosomal translation, which is indispensable for cell survival and thus provide potential targets for the development of a new class of antibiotics.
Data analysis using bioinformatic tools will be developed in conjunction with the CCP group to help exploit the mid- and high-throughput results obtained by IGDR teams.
As part of the "Genomic Biology and Cancer" grouping, members from the six constituent teams meet every two months to discuss general strategies and methodological questions. In particular, the grouping is aimed at accelerating knowledge transfer within and between the teams, as well as improving research techniques, thus increasing the research potential of the Institute as a whole.
A few topics that will require particular attention have been identified:
- Nanopore sequencing:
Thanks to a recently acquired MinION sequencing device from Oxford Nanopore, researchers from the IGDR can now access long-read as well as direct RNA and DNA sequencing (i.e. without amplification). However, despite a very active user community, its data processing technology is still being refined. This is especially the case for discriminating modified bases (such as 5-mC and 5-hmC) in templates. Computer scientists from the ANDRE, PAILLARD and SALBERT teams are working together to set up data-processing pipelines.
- Single-cell sequencing:
Tumour heterogeneity requires single-cell sequencing methods for the characterization of cellular clones within samples. But tumour biology is not the only instance in which single-cell analysis can be useful. Indeed, cell differentiation of pluripotent cells in culture might generate multiple cell types with distinct epigenomes. In addition, single-cell sequencing could help us understand how replication origins are selected by the cell. Teams are therefore thinking together about how to implement such methods within the IGDR.
- Cryo-Electron Microscopy:
Cryo-EM is the technique of choice for studying the 3D structures of large macromolecular complexes, as there is no upper size limit. In the IGDR method, workflow shall follow a two-step procedure. Structural analysis of each isolated complex will first be performed locally, from wet biochemistry to the cryo-EM analysis using an in-house Tecnai G2 Sphera LaB6 200kV microscope. Once a low/medium resolution 3D map of complexes is established, the most promising samples will be processed in open-access facilities such as at FRISBI, which is equipped with FEI Titan Krios microscopes and direct electron detectors.
