RNA degradation

Group leader : Dominique GAGLIARDI

Research area

RNA degradation stands among the most powerful processes to control gene expression. Diverse and intricate RNA decay pathways cooperate:

  • to ensure that the degradation of coding and non-coding RNAs is tightly regulated in response to developmental or environmental stimuli
  • to eliminate defective transcripts (RNA quality control)
  • to counterbalance loose transcriptional control by degrading transcripts generated from intergenic regions (RNA surveillance)
  • to fight pathogens such as viruses.

Our main objectives are to identify key actors of RNA degradation pathways in plants, and to determine their impact on genome expression, development or stress response. Our studies currently focus on new co-factors of the RNA exosome, on enzymes that adenylate or uridylate RNAs and on new factors associated to P-bodies and decapping activators. Finally, we address the roles of RNA degradation pathways during viral infections.

Our main experimental strategies include forward and reverse genetics in the model plant Arabidopsis thaliana, protein biochemistry approaches coupled to mass spectrometry analyses, and new high-throughput techniques based on Illumina and Nanopore sequencing to identify 3’ modifications of transcripts.

Key funding of our current research includes the NetRNA LabEx (2011-2028) and the ANR grants 3’modRN (2015-2021) and URIVir (2021-2025).

Projects

The RNA exosome and its co-factors

Project manager: Heike LANGE

The RNA exosome is a multisubunit complex in charge of the 3’-5’ processing or degradation of a wide range of RNA substrates. The core of the exosome is present in both the cytosol and the nucleus and associates to various co-factors that modulate its activity and mediate the recognition of its RNA substrates. Our main objectives are to identify new co-factors of the RNA exosome and to characterize their roles in gene expression and plant development.

Team members involved: Laurie Marsan, Heike Lange & Dominique Gagliardi

Uridylation of mRNAs

Project manager: Hélène ZUBER

The uridylation of mRNAs is emerging as a conserved process in Eukaryotes and we are just beginning to understand the impact of this 3’ modification on gene expression. We aim to decipher all molecular steps leading to mRNA uridylation and its multiple consequences on degradation and translational repression. We also investigate the biological importance of mRNA uridylation during seed development and in response to various stresses.

Team members involved: Quentin Simonnot, Pietro Giraudo, Hélène Zuber & Dominique Gagliardi

Uridylation of viral RNAs

Project managers: Hélène ZUBER, Damien GARCIA

We explore the roles of uridylation in the metabolism of viral RNAs. A part of this project is developed in collaboration with the team of Olivier Lemaire located at the INRAE Centre Grand Est in Colmar.

Team members involved: Anne-Caroline Joly, Damien Garcia, Hélène Zuber & Dominique Gagliardi

Novel components of P-bodies

Project manager: Damien GARCIA

We have recently identified an endoribonuclease that is associated with decapping activators and Processing-bodies (P-bodies), a class of RNA granules highly conserved in Eukaryotes. We investigate its involvement in the regulation of gene expression, plant development and stress response. We also study other new components of P-bodies to discover their functions in RNA metabolism and plant responses to environmental stimuli

Team members involved: Aude Pouclet, Tiphaine Chartier & Damien Garcia

Members