Macromolecular Interaction Genetics - CNRS URA2171  

  MEMBERSJacquier, Alain, CNRS, DR1 / Fromont-Racine, Micheline, CNRS, DR2 / Saveanu Cosmin , Institut Pasteur, research scientist (IP) / Neil, Helen, Post-doc / Demoinet, Emilie, PhD student / Yao, Yanhua, PhD student / Zemam, Kenza, PhD student / Malabat, Christophe bioinformatics engineer / Decourty, Laurence, Technician / Labouise, Odile, Office staff

  Annual Report

The unifying theme of the laboratory is the study of eukaryotic RNA cellular metabolism in a model organism, the yeast S. cerevisiae. Several intertwined topics have evolved in our laboratory from this general theme. We described molecular mechanisms that are essential for ribosome formation, discovered novel cellular RNAs (CUTs), identified novel mRNA degradation factors and developed a novel genome-scale genetic screen.

Ribosome biogenesis

Ribosomes are abundant protein factories and their formation is an essential process, highly conserved in eukaryotes, which may consume up to 80% of the metabolic energy in proliferating cells. While ribosome formation starts into the nucleolus, it continues into the nucleoplasm and ends into the cytoplasm. This pathway requires the rRNA, transcribed under the form of precursors, ribosomal proteins that have to be imported into the nucleus, and a large number of pre-ribosomal factors. In contrast to the ribosomal proteins, which associate early to the particles and remain tightly bound to the mature subunits, the pre-ribosomal factors bind only transiently to the assembly intermediates and must dissociate to allow formation of the final, functional ribosomal particles.

During the past few years, we contributed to the identification and the characterisation of many of these early, intermediate and late pre-60S factors and to the establishment of general ribosome assembly mechanisms. We have recently focused our studies on the export of pre-60S particles and recycling of the shuttling pre-ribosomal factors with a focus on the links between the pre-60S particles and pre-60S factors and the nucleocytoplasmic machinery such as the nucleopore and the karyopherins.

CUTs - Cryptic Unstable Transcripts.

A few years ago, in collaboration with three other laboratories, we described the existence of a novel class of ubiquitous transcripts that are normally very efficiently degraded by the combined action of a poly-adenylation complex (TRAMP) and of the nuclear exosome (La Cava et al., Cell 2005; Wyers et al., Cell 2005). These transcripts, collectively known as CUTs - for Cryptic Unstable Transcripts, are very abundant in mutant strains that lack the degradation or poly-adenylation activities. We have now generated the genomic map of CUTs, which suggests that the majority of these transcripts arise from cryptic start sites rather than cryptic promoters. This reveals properties of the transcription process which were not previously known to occur at such a large scale and that appear to be used in some cases for a novel type of transcription regulation.

Genetic interaction networks.

A fundamental aim of genetics is to predict the results of altering a gene function on the observed phenotype. Since genes do not “act” in isolation, but rather via the interposed interaction of their expression products, we tried to obtain insights into gene function on a genomic scale by measuring the growth impact of combining mutations in S. cerevisiaecells. To obtain quantitative and sensitive measurements of these genetic interactions we developed a novel method, called GIM for Genetic Interactions Mapping, and used it in a pilot experiment covering 140 000 tested combinations of non-essential gene deletions (Decourty et al., PNAS 2008). Surprisingly, a important amount of functional information could be extracted from a large number of weak measured effects. Moreover, we could indirectly link a large number of genes unrelated to the mutations used for screening, giving the method full potential for unexpected discoveries. In addition, a lower number of strong effects, classically described as synthetic lethality, allowed the identification of novel mRNA degradation factors. Using variants of essential genes and a broad selection of mutants affecting various cellular pathways we now try to describe a significant fraction of the complete yeast genetic “interactome”.

Keywords: RNA metabolism, RNA degradation, ribosome biogenesis, genetic screen, Saccharomyces cerevisiae


Lebreton, A., C. Saveanu, L. Decourty, J. C. Rain, A. Jacquier, and M. Fromont-Racine.2006. A functional network involved in the recycling of nucleocytoplasmic pre-60S factors. J Cell Biol173:349-60

LaCava, J., J. Houseley, C. Saveanu, E. Petfalski, E. Thompson, A. Jacquier, and D. Tollervey.2005. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell121:713-724

Wyers, F., M. Rougemaille, G. Badis, J. C. Rousselle, M. E. Dufour, J. Boulay, B. Régnault, F. Devaux, A. Namane, B. Séraphin, D. Libri, and A. Jacquier.2005. Cryptic Pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell121:725-737

Badis, G., C. Saveanu, M. Fromont-Racine, and A. Jacquier.2004. Targeted mRNA degradation by deadenylation-independent decapping. Mol Cell15:5-15

Galy, V., O. Gadal, M. Fromont-Racine, A. Romano, A. Jacquier, and U. Nehrbass.2004. Nuclear Retention of Unspliced mRNAs in Yeast Is Mediated by Perinuclear Mlp1. Cell116:63-73

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Activity Reports 2007 - Institut Pasteur
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