During an immune response activated B cells undergo rapid clonal expansion and concurrently generate diverse cellular fates. Understanding of the complex molecular regulation of these processes in single cells, and its interaction with the concurrent rapid cell division during clonal expansion, remains incomplete.
Here, we combined a novel high-throughput proliferation-based lineage tracing technique with molecular analysis of B lymphocytes to study class switch recombination (CSR) within the Igh locus, and differentiation to antibody-secreting cells across thousands of clonal families.
We found that cell division and differentiation dynamics were strongly correlated within clones. In striking contrast, CSR was stochastically regulated across cells sharing a common ancestry.
We determined that the mechanism of clonally stochastic CSR is driven by three probabilistic molecular events. This comprises 1) significant intraclonal variation in the expression of the DNA-editing enzyme activation-induced cytidine deaminase (AID), 2) the independent and stochastic transcription of multiple germline long non-coding RNAs within the Igh locus in single cells, and 3) the random accumulation of AID-induced mutations within Igh switch regions across expanding family trees.
These results establish that antibody diversification by CSR is regulated by a stochastic clonal program driven by independent probabilistic molecular events.