Séminaires virtuels

Séminaires Online 

Dr. Wojtek Galej (Département de Biologie Structurale, EMBL Grenoble)

Jeudi 13 Juin 2024 à 11h


Titre: Structural studies of the intron recognition by the human spliceosome

Abstract:
The spliceosome is a multi-megadalton RNA-protein complex responsible for the removal of non-coding introns from pre-mRNAs. Due to its complexity and dynamic nature, it has proven to be a challenging target for structural studies. Developments in single particle cryo-EM have paved the way towards structural characterisation of the splicing machinery. Despite tremendous progress, many aspects of spliceosome structure and function remain elusive. In particular, the events leading to the definition of exon-intron boundaries, alternative and non-canonical splicing events, and cross-talk with other cellular machines. During my talk, I will summarise recent progress in the structural and functional 
analysis of the human spliceosome with a particular focus on the early events during intron recognition.

Pr. Dr. Michelle Scott (Département de Biochimie et de Génomique Fonctionnelle, Université de Sherbrooke, Canada)

Jeudi 25 Avril 2024 à 15h


Titre: Small nucleolar RNAs follow their own rules: characterization of their expression determinants and non-canonical functions

Abstract:
Small nucleolar RNAs (snoRNAs) are non-coding RNAs well known for their role in ribosome biogenesis, many serving as guides for the site-specific modification of ribosomal RNA. The last two decades have demonstrated additional regulatory functions for subsets of snoRNAs in gene expression regulation the extent of which is still unknown. Another intriguing characteristic of snoRNAs is their diverse expression strategies across eukaryotic species, which include expression from their own promoter as well as embedding in and co-maturation with host genes. Transcriptomic profiling analyses have revealed unexpected expression patterns and binding partners for snoRNAs. Based on these findings, we used machine learning approaches to identify their most likely expression determinants, providing insight into their evolution and recommendations as to their genomic annotations. In parallel to this study on snoRNA expression, to characterize the extent of snoRNA functionality, we used an integrative network biology approach combining large-scale RNA-RNA and RNA-protein interaction datasets to define the snoRNA interactome, identifying cis and trans targets of snoRNAs with evidence of functional relationships, some of which were chosen for experimental validation. These studies provide insight into the breadth and depth of functionality of these highly abundant and central regulatory RNAs.

Dr. Clément Chapat (Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France)

Jeudi 1er Février 2024 à 11h

Titre: Exploring how physical intimacy between translation apparatus and mRNA silencing machineries shapes the proteome
 
Abstract:
The post-transcriptional regulations of gene expression represent a new terra incognita to be explored in biology. Post-transcriptional silencing mechanisms modulate mRNA stability and translation, contributing to the rapid and flexible control of protein synthesis. This phenomenon mainly relies on the repressive activity of the CCR4-NOT deadenylase complex which can be mobilized by microRNAs, RNA-binding proteins and mRNA modifications. Recent data showed that CCR4-NOT displays a selective activity based on the codon composition of the targeted mRNA. Our recent preliminary data shed light on how CCR4-NOT dictates the fate of mRNAs through targeting the translating ribosomes. Why and how CCR4-NOT promotes a bidirectional modulation of mRNA translation and decay based on codon usage remains an outstanding question. With this in mind, our research at the Centre for Integrative Biology of Toulouse aims to investigate the mechanisms that link the translation apparatus with mRNA silencing machineries, and how this physical intimacy drives cell-fate decisions. In particular, we seek to set up an integrated experimental framework to measure the impact of ribosome-targeting by CCR4-NOT on translational landscapes. Altogether, our results open a fascinating window into our understanding of how a physical intimacy between mRNA silencing machineries and translation apparatus shapes the ever-changing swarm of proteins that differs from cell to cell.

Dr. Karina Jouravleva (Phil Zamore's lab, UMass, USA; lauréate 2023 des concours ATIP-Avenir et CRCN-CNRS, LBMC, ENS-Lyon)

Jeudi 12 Octobre 2023 à 11h

Titre: Specificity and function of Argonaute protein-mediated pathways
 
Abstract:
In plants and animals, microRNAs (miRNAs) direct Argonaute (Ago) proteins to repress mRNA expression. MiRNAs influence every physiological process, and dysregulated miRNAs have been linked to human diseases including cancer. Because miRNAs confer binding specificity to Ago proteins, accurate miRNA production is a pre-requisite for miRNA function. MiRNAs are processed from the double-stranded stem of hairpin precursor RNAs (pre-miRNAs) by the ribonuclease Dicer.  In flies, the Dicer-1 (Dcr-1) partner protein Loquacious-PB (Loqs-PB) enhances the efficiency of miRNA production and the choice of cleavage sites by Dcr-1, producing miRNAs with target specificities different from those made by Dcr-1 alone. In the first part of my talk, I will show the cryo-electron microscopy structures of Dcr-1 in complex with Loqs-PB before binding a pre-miRNA, upon substrate binding in a catalytic competent state, and after dicing but before product release. Our reconstructions show how the domains of Dcr-1:Loqs-PB recognize the pre-miRNA to ensure its accurate and efficient processing and highlight the conformational changes triggered by pre-miRNA cleavage that promote product release.
Once produced, miRNAs bind targets through their seed sequence—guide bases g2–g7. As few as six base pairs can mediate high affinity interactions, but some miRNAs gain considerable binding energy from non-seed nucleotides. Moreover, mammalian Ago proteins consist of four paralogs AGO1–4, which are expressed in different proportions across various cell types. AGO2 is the most studied paralog, and its binding specificity has been well characterized in vitro. However, affinity measurements are unavailable for AGO1, AGO3 and AGO4; therefore, their individual contributions to miRNA-mediated silencing remain uncharacterized. In the second part of my talk, I will present our experimental strategies to measure the equilibrium binding properties and kinetic parameters of Ago proteins. Using RNA Bind-n-Seq and Co-localization Single Molecule Spectroscopy, we have begun to define the target interactions of the four mammalian Argonaute proteins. Our quantitative measurements should allow prediction of complex and dynamic miRNA-mRNA regulatory networks and may facilitate the development of siRNA, miRNA, and antagomir therapeutics with high potency and target specificity.

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