Role of DEAD-box RNA helicase 1 in the mechanism of class switch recombination at the immunoglobulin heavy-chain locus
Lead Research Organisation:
University of Cambridge
Department Name: School of Biological Sciences
Abstract
PhD project strategic theme: Understanding the rules of life
B cells have the unique ability to produce a tailored and highly specific antibody response against a virtually limitless range of antigens, which is possible due to diversification of antibody genes. As B cells differentiate into antibody secreting cells, gene deletional and recombinatorial events occur at the IgH locus by a mechanism known as class switch recombination (CSR). CSR exchanges the exon encoding the constant region of the IgH chain (CH exon) for an alternative antibody isotype (e.g. IgG), thereby defining the effector function of antibodies. At the molecular level, CSR depends on transcription of long non-coding RNA (switch RNA) initiated upstream of each CH exon undergoing recombination. Due to the G-richness and highly repetitive nature of switch RNA sequences, these transcripts can fold into G-quadruplex structures (G4 RNA) and can stably hybridize to the template DNA strand forming R-loop structures. Both G4 RNA and R-loop structures have been implicated in targeting the mutagenic enzyme activation-induced cytidine deaminase (AID) to the IgH locus, to initiate CSR.
The Ribeiro group studies how RNA binding proteins (RBPs) regulate DNA recombination at Ig loci. In particular, we are interested in the role of DEAD-box RNA helicases, a large family of RBPs that utilize ATP hydrolysis to remodel RNA structures or RNA-protein interactions. The Ribeiro group have previously shown that DEAD-box RNA helicase 1 (DDX1) binds to G4 RNA and converts it into Rloops, thus targeting AID and promoting CSR (Ribeiro de Almeida et al., 2018). This PhD project aims to understand the role DDX1 and G4 RNA play downstream of AID targeting. Our unpublished data suggests DDX1 participates in the DNA repair of AID-induced DNA double-strand breaks (DSBs). Importantly, inappropriate targeting of AID to non-Ig hotspots (off-target genes) and aberrant DSB repair leads to the development of B cell lymphoma. Therefore, a related question is whether a DDX1/G4 RNA mechanism of AID targeting is associated with B cell lymphomagenesis. To address these questions, we will 1) characterize the molecular mechanisms by which DDX1 participates in DSB repair; 2) investigate if DDX1 is implicated in DSB repair pathway choice and associated genome
instability; 3) determine how DDX1's role in CSR relates to B-cell activation during an immune response. These studies will provide new insight into RNA-mediated mechanisms controlling CSR, which deregulation can result in the development of immune disease or B-cell lymphomagenesis.
B cells have the unique ability to produce a tailored and highly specific antibody response against a virtually limitless range of antigens, which is possible due to diversification of antibody genes. As B cells differentiate into antibody secreting cells, gene deletional and recombinatorial events occur at the IgH locus by a mechanism known as class switch recombination (CSR). CSR exchanges the exon encoding the constant region of the IgH chain (CH exon) for an alternative antibody isotype (e.g. IgG), thereby defining the effector function of antibodies. At the molecular level, CSR depends on transcription of long non-coding RNA (switch RNA) initiated upstream of each CH exon undergoing recombination. Due to the G-richness and highly repetitive nature of switch RNA sequences, these transcripts can fold into G-quadruplex structures (G4 RNA) and can stably hybridize to the template DNA strand forming R-loop structures. Both G4 RNA and R-loop structures have been implicated in targeting the mutagenic enzyme activation-induced cytidine deaminase (AID) to the IgH locus, to initiate CSR.
The Ribeiro group studies how RNA binding proteins (RBPs) regulate DNA recombination at Ig loci. In particular, we are interested in the role of DEAD-box RNA helicases, a large family of RBPs that utilize ATP hydrolysis to remodel RNA structures or RNA-protein interactions. The Ribeiro group have previously shown that DEAD-box RNA helicase 1 (DDX1) binds to G4 RNA and converts it into Rloops, thus targeting AID and promoting CSR (Ribeiro de Almeida et al., 2018). This PhD project aims to understand the role DDX1 and G4 RNA play downstream of AID targeting. Our unpublished data suggests DDX1 participates in the DNA repair of AID-induced DNA double-strand breaks (DSBs). Importantly, inappropriate targeting of AID to non-Ig hotspots (off-target genes) and aberrant DSB repair leads to the development of B cell lymphoma. Therefore, a related question is whether a DDX1/G4 RNA mechanism of AID targeting is associated with B cell lymphomagenesis. To address these questions, we will 1) characterize the molecular mechanisms by which DDX1 participates in DSB repair; 2) investigate if DDX1 is implicated in DSB repair pathway choice and associated genome
instability; 3) determine how DDX1's role in CSR relates to B-cell activation during an immune response. These studies will provide new insight into RNA-mediated mechanisms controlling CSR, which deregulation can result in the development of immune disease or B-cell lymphomagenesis.
