Investigating Mechanisms of DNA Double Strand Break Joining of Switch Regions During IgH Class Switch Recombination

During B cell development, RAG endonuclease cleaves immunoglobulin heavy chain (IgH) V, D, and J gene segments and orchestrates their fusion as deletional events that assemble a V(D)J exon in the same transcriptional orientation as adjacent Cμ constant region exons. In mice, six additional sets of constant region exons (CHs) lie 100–200 kilobases downstream in the same transcriptional orientation as V(D)J and Cμ exons. Long repetitive switch (S) regions precede Cμ and downstream CHs. In mature B cells, class switch recombination (CSR) generates different antibody classes by replacing Cμ with a downstream CH. Activation-induced cytidine deaminase (AID) initiates CSR by promoting deoxycytidine deamination lesions within Sμ and a downstream acceptor S-region; these lesions are converted into DNA double-strand breaks (DSBs) by general DNA repair factors which are then joined by end-joining pathways. Productive CSR must occur in a deletional orientation by joining the upstream end of an Sμ DSB to the downstream end of an acceptor S-region DSB. However, the relative frequency of deletional to inversional CSR junctions has not been measured. Thus, whether orientation-specific joining is a programmed mechanistic feature of CSR as it is for V(D)J recombination and, if so, how this is achieved is unknown. To address this question, we adapt high-throughput genome-wide translocation sequencing (HTGTS) into a highly sensitive DSB end-joining assay and apply it to endogenous AID-initiated S-region in mouse B cells. We show that CSR is programmed to occur in a productive deletional orientation and does so via an unprecedented mechanism that involves in cis IgH organizational features in combination with frequent S-region DSBs initiated by AID. We further implicate ATM-kinase-dependent DSB-response (DSBR) factors including histone variant H2AX, 53BP1 and its associated effector protein Rif1 in enforcing this mechanism. We go on to use HTGTS to study influence of different DSBR factor deficiencies on the structure of CSR junctions between AID-initiated DSBs in the 5' portion of the donor Sμ region to those across the length of downstream acceptor S regions. Based on analyses of thousands of switch junctions, we find that absence of DSBR factors leads to varying increases in micro-homology (MH)-mediated junctions, with 53BP1-deficiency having the greatest increase. However, while translocation junctions between Cas-9/gRNA-induced DSB in c-myc to AID-initiated S region DSBs in ATM- or 53BP1-deficient B cells show similar biases in MH-usage to those observed in the context CSR junctions, translocation junctions to other general DSBs genome-wide had no MH-usage increase in ATM-deficient cells and only a modest increase in 53BP1-deficient cells. We discuss these findings with respect to potential roles of AID-initiated DSBs in S regions to be especially prone to MH-usage potentially due to their increased resection along with their highly repetitive nature that provides abundant micro-homologous sequence.Medical Science