Orientation regulation of class switch recombination in human B cells

We developed a linear amplification-mediated high-throughput genome-wide translocation sequencing method to profile immunoglobulin (Ig) class switch recombination (CSR) in human B cells in an unbiased and quantitative manner. This method allowed us to quantify CSR resulting from either deletional recombination or inversion, for each Ig class/subclass. Our data revealed that vast majority of CSR junctions (>90%) detected in healthy controls were due to deletional recombination. We further identified two major CSR junction signatures in B cells from healthy donors. Signature-1 primarily consists of deletional recombination (90%), marked by a dominance of Smu-Sgamma junctions (76%). Signature-2 is characterized by an IgA-dominant pattern (96%) and relies exclusively on deletional recombination (99%). Notably, almost all CSR junctions found in patients with defects in the classical non-homologous recombination (c-NHEJ) pathway aligned with signature-2. Our findings thus suggest that, as demonstrated in mice, CSR in human B cells is programmed for deletional recombination. Importantly, we found that the c-NHEJ machinery and the distinct features of switch regions are crucial in determining the CSR orientation in human B cells.