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. To gain molecular insights into this fate determination mechanism we studied the interactions of CBC-ARS2 with three RNA effectors - PHAX involved in snRNA export, NCBP3 involved in mRNA export and ZC3H18 mediating RNA degradation.

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).