Projects

RNA biogenesis regulation
RNA polymerase II (Pol II) transcribes key RNA classes, including protein-coding mRNAs, regulatory RNAs such as miRNAs, or small nuclear RNAs (snRNAs), which are all processed in the nucleus and often exported to the cytoplasm. However, Pol II also generates large amounts of nonproductive transcripts, such as promoter upstream transcripts (PROMTs), enhancer RNAs (eRNAs), prematurely terminated transcripts or other unwanted RNAs, that must be rapidly degraded. Accumulation of such RNAs could disrupt essential processes such as transcription and genome stability maintenance. How cells distinguish between functional and unwanted nascent transcripts, and determine their fate, remains poorly understood.
During early transcription, nascent transcripts acquire an m7G-cap at their 5’ end, which is rapidly bound by the nuclear cap-binding complex (CBC), composed of CBP80 and CBP20, and involved in essentially every step of gene expression. With its key partner ARS2, CBC forms the CBC-ARS2 (CBCA) complex, a central regulator of transcriptional and post-transcriptional fate decisions. Whether transcripts undergo processing, export or degradation depends on dynamic CBCA interactions with mutually exclusive RNA biogenesis regulators called effectors.

Figure : RNA effectors compete for binding to CBC-ARS2.

To better understand the molecular details underlying this RNA fate determination mechanism, together with Stephen Cusack (EMBL Grenoble) and Torben Jensen (Aarhus University), we structurally and biochemically characterized how several effectors, including the snRNA export factor PHAX, the mRNA export factor NCBP3, and the RNA-targeting NEXT complex subunit ZC3H18, compete for their interactions with both CBC and ARS2. Our work revealed that these effectors interact with ARS2 via a short linear motif called ARM (ARS2-recognition motif) and with the CBC via a helix carrying a conserved tryptophan residue (Foucher et al, Nat Commun 2022, Dubiez et al, Cell Rep 2024).

Figure : Cryo-EM structure of CBC bound to a tryptophan-containing helices of PHAX and NCBP3. c. In vitro and in vivo validated AlphaFold model of CBC bound to a tryptophan-containing helix of ZC3H18.

We have now also determined a cryo-EM structure of the snRNA export complex, an example of a post fate-decision, committed assembly, comprising phosphorylated PHAX, CBC, CRM1, Ran-GTP and capped RNA. The structure reveals how PHAX bridges the CBC-bound capped RNA to the CRM1- RanGTP export factor while also significantly reinforcing cap dinucleotide binding. Our findings demonstrate that snRNA export complex formation requires synergistic binding of all its components, which in turn displaces ARS2 from the CBC, and commits the snRNA for export (Dubiez et al., Nat Struct Mol Biol 2025, see also News & Views)

Figure : A schematic model of snRNA export mediated by the snRNA export complex b. Ribbon representation of the snRNA export complex. RNA and GTP are shown as sticks.

Epigenetic regulation
In eukaryotes, DNA is packaged as chromatin, whose dynamics and chemical modifications control access to and interpretation of genetic information in processes such as transcription and DNA repair. Post-translational histone modifications, notably lysine acetylation and methylation, alter chromatin structure and/or recruit or repel effector proteins.
In our work, we have been using an interdisciplinary approach combining biochemical and structural analyses with cell biology and genetics to provide mechanistic insights into the mode of action of important chromatin-modifying complexes, including histone acetyltransferases and methyltransferases, that control epigenetic processes and are often deregulated in human diseases.

Epigenetic regulation of meiotic recombination
Sexual reproduction depends on meiosis, a specialized cell division that produces haploid cells destined to become gametes. At the onset of meiotic prophase I, a number of DNA double-strand breaks (DSBs) is formed at preferred genomic sites called hotspots. These DSBs are repaired by homologous recombination, forming connections between maternal and paternal chromosomes essential for accurate segregatio. Our work, in collaboration with Bernard de Massy’s group (IGH Montpellier), addressed two key questions : How are meiotic hotspots determined, and how is DSB formation regulated ? The DSBs occur at specific locations called hotspots and involves the histone methyltransferase PRDM9. Our structure-function studies showed that the PRDM9 catalytic activity is essential for DSB formation at PRDM9-binding sites (Wu et al, Cell Rep. 2013 ; Diagouraga et al, Mol Cell 2018) The actual DNA cut is performed but the Spo11 catalytic complex that requires several accessory factors including the REC114-MEI4-IHO1 complex called the pre-DSB recombinosome complex. We biochemically and structurally characterized pre-DSB recombinosome complex and showed how it connects to the catalytic complex (Nore et al, Nat. commun 2022 ; Laroussi et al, EMBO J 2023).