RNA exosome drives B cell development via noncoding RNA processing mechanisms

Le 24 avril 2023 à 14h00 Séminaire

B cell development is linked to successful V(D)J recombination, allowing B cell receptor expression and B cell migration to secondary lymphoid organs. Antigen encounter induces activation-induced deaminase (AID) expression, necessary for class switch recombination (CSR) and somatic hypermutation (SHM). Germline noncoding RNAs (ncRNAs) are produced at immunoglobulin (Ig) loci during V(D)J recombination, CSR, and SHM, and we noticed increased expression of RNA exosome subunits at these stages in mouse B cells. Thus, we investigated the relationship between ncRNA production and RNA exosome activity during the different steps of B cell recombination.

First, we generated mouse models harboring a B cell-specific cre allele (Mb1^cre), coupled to conditional inversion-deletion (COIN) alleles of RNA exosome components (Exosc3,Exosc10, or Dis3). B cell developmental blockade at the pro-B cell stage was observed in the different knockout mice, overlapping with a lack of productive rearrangements of VDJ genes at the Ig heavy chain (Igh). This unsuccessful recombination prevented differentiation into pre-B cells, with accumulation of ncRNAs and up-regulation of the p53 pathway. Introduction of a prearranged Igh VDJ allele partly rescued the pre-B cell population in Dis3-deficient cells, although VJ recombination defects were observed at Ig light chain kappa (Igk), preventing subsequent B cell development.

Second, we studied the role of the RNA exosome in activated B cells and its interplay with AID activity for efficient CSR and SHM.In DIS3-deficient B cells, integrity of the Igh locus in its topologically associating domain (TAD) is affected, with accumulation of DNA-associated RNAs flanking CTCF-binding elements (CBEs), decreased CTCF binding to CBEs and disorganized cohesin localization. DIS3-deficient B cells also accumulate AID-mediated asymmetric nicks, altering SHM patterns and increasing microhomology-mediated end-joining DNA repair. Altered mutation patterns and Igh architectural defects in DIS3-deficient B cells lead to decreased CSR but increased chromosomal translocations.  

These data demonstrated that the RNA exosome complex is important for Igh and Igk V(D)J recombination, efficient CSR, and accurate distribution of AID-mediated mutations. Thus, our observations establish the relevance of RNA processing for optimal diversification at Ig loci during B cell development.