Genome-wide AID target loci in BL2 cells

Activation-induced cytidine deaminase (AID) is required for both somatic hypermutation (SHM) and class-switch recombination (CSR) in activated B cells. AID is also known to target non-immunoglobulin genes and introduce mutations or chromosomal translocations, eventually causing tumors. To identify as-yet-unknown AID targets, we screened early AID-induced DNA breaks using two independent genome-wide approaches. Along with known AID targets, this screen identified a set of novel genes (SNHG3, MALAT1, BCL7A, and CUX1), and confirmed that these new loci accumulated mutations as high as Ig locus after AID activation. Moreover, these genes share three important characteristics with the immunoglobulin gene: translocations in tumors, repetitive sequences and the epigenetic modification of chromatin by H3K4 trimethylation in the vicinity of cleavage sites. BL2 cells expressing JP8Bdel-ER, an AID mutant lacking the C-terminal 16 residues, fused with the hormone-binding domain of the estrogen receptor (ER) were treated with tamoxifen (OHT) for 3 hours to induce AID activation. AID-induced DNA breakage was labeled with biotinilated linker. Comparison of OHT treated vs. non-treated samples.