UC San Diego

During VDJ recombination, pro-B cells rearrange the variable regions of their immunoglobulin heavy chain (Igh) loci to produce antibodies with unique antigen binding specificities. Long-range genomic interactions which allow for incorporation of a diverse selection of V genes into the antibody repertoire is crucial for robust immunity. The work in this thesis sought to understand how Igh genes find each other across vast genomic distances to undergo recombination. To do this, we imaged distally located V and DJ genomic regions in live pro-B cells. We paired this approach with targeted depletion and specific inhibition of individual components of the chromatin environment. This allowed us to determine how chromatin structure of the Igh locus relates to the chromatin motion of distally located V and DJ genomic regions. Through this approach, we identified distinct levels of chromatin confinement at the Igh locus. Transcription locally confines V and DJ genomic regions, reducing their motion and stabilizing interactions between spatially proximal regions. Cohesin loops globally confine V and DJ regions, bringing the regions into close spatial proximity and substantially reducing their chromatin motion. Estimations of the times to encounters for these V and DJ regions revealed that even small changes in chromatin motion can have large effects on interaction frequencies. These findings have implications not only on the physical mechanism of VDJ recombination, but also chromatin dynamics more broadly.