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. We focus on new co-factors of the RNA exosome, the main 3’-5’ exoribonucleolytic complex in Eukaryotes, and on components of the non-sense mediated decay pathway. We aim to understand their roles in RNA substrate recognition and degradation. We are also particularly interested in a class of enzymes that adenylate or uridylate RNAs and we study how these 3’ modifications impact RNA’s fate. Finally, we address the roles of RNA degradation pathways during RNA virus infections.

New components of RNA decay and their functions are identified through forward and reverse genetics strategies in the model plant Arabidopsis thaliana, or by protein biochemistry approaches coupled to mass spectrometry analyses. We also develop new high-throughput techniques to identify 3’ modifications of transcripts.

Key fundings of our current research include the NetRNA LabEx (ANR-2010-LABX-36 ; 2011-2020) and the 3’modRN ANR grant (ANR-15-CE12-0008 ;  2015-2020).

Projects

The RNA exosome and its co-factors

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. We study key features of plant RNA exosome complexes, such as the functional specialization of co-factors encoded by small multigenic families, the phosphorolytic activity of the core exosome or the characterization of novel types of co-factors and their impact on gene expression and plant development.

Team members involved: Heike Lange and Dominique Gagliardi

RNA uridylation

The uridylation of non-coding and coding RNAs 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 of target mRNAs. We also investigate the impact of mRNA uridylation in the stress response of plants.

Team members involved: Hélène Zuber, Hélène Scheer, Caroline de Almeida and Dominique Gagliardi

Interrelations between RNA decay pathways and RNA viruses

Project manager: Damien GARCIA

We explore the influence of RNA degradation during RNA virus infection. We previously described the role of Nonsense-Mediated Decay (NMD) in viral restriction. We currently study the functions of UPF1, a key NMD factor, and novel P-body components found associated with UPF1. We also evaluate the involvement of other important factors involved in RNA metabolism during infection. These approaches aim to uncover novel cellular components modulating viral multiplication.

Team members involved: Marlène Schiaffini, Marie Bonnin & Damien Garcia

Members

Selected publications

  • LANGE H., NDECKY S., GOMEZ-DIAZ C., PFLIEGER D., BUTEL N., ZUMSTEG J., KUHN L., PIERMARIA C., CHICHER J., CHRISTIE M., KARAASLAN E.S., LANG P.L., WEIGEL D., VAUCHERET H., HAMMANN P. and GAGLIARDI D.

    RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis

    Nature Communications, 10:3871, 2019. | DOI : 10.1038/s41467-019-11807-4DOI logo

  • CHICOIS C., SCHEER H., GARCIA S., ZUBER H., MUTTERER J., CHICHER J., HAMMANN P., GAGLIARDI D. and GARCIA D.

    The UPF1 interactome reveals interaction networks between RNA degradation and translation repression factors in Arabidopsis

    Plant Journal, 96:119-132, 2018. | DOI : 10.1111/tpj.14022DOI logo

  • SIKORSKA N., ZUBER H., GOBERT A., LANGE H. and GAGLIARDI D.

    RNA degradation by the plant RNA exosome involves both phosphorolytic and hydrolytic activities

    Nature Communications, 8:2162, 2017. | DOI : 10.1038/s41467-017-02066-2DOI logo

  • SCHEER H., ZUBER H. and GAGLIARDI D.

    Uridylation earmarks mRNAs for degradation... and more.

    Trends in Genetics, 32(10):607-19, 2016. | DOI : 10.1016/j.tig.2016.08.003DOI logo

  • ZUBER H., SCHEER H., FERRIER E., SEMENT F.M., MERCIER P., STUPFLER B. and GAGLIARDI D.

    Uridylation and PABP cooperate to repair mRNA deadenylated ends in Arabidopsis.

    Cell Reports, 14(11):2707-17, 2016. | DOI : 10.1016/j.celrep.2016.02.060DOI logo