AID-induced translocation libraries in MEFs. Mus musculus

Activation-induced cytidine deaminase (AID) initiates class switch recombination (CSR) and somatic hypermutation (SHM) by deaminating cytosine residues in immunoglobulin (Ig) genes. At a lower frequency, AID also causes collateral DNA damage at non-Ig loci, including genes that are rearranged or mutated in B cell lymphoma. Precisely how AID is recruited to these off-target sites is not entirely understood. To gain further insight into how AID selects its targets we compared AID-mediated translocations in two different cell types, B cells and mouse embryonic fibroblasts (MEFs). AID-mediated translocations in MEFs were captured by TC-Seq, a technique that combines PCR and deep sequencing, to document chromosome rearrangements from a defined I-SceI site to AID breaks genome-wide. Primary AID-deficient MEFs, harboring I-SceI sites at Myc and Igh (MycI IghI AID-/-), were infected with a retrovirus encoding I-SceI alone or I-SceI and AID linked by a self-cleaving 2A peptide (I-SceI-2A-AID). The control is retroviral infection with only I-SceI overexpression.