A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets.. Mus musculus

Activation Induced Deaminase (AID) initiates somatic hypermutation (SHM) and class switch recombination (CSR) in germinal center (GC) B cells through the deamination of deoxycytidine residues (dC) into deoxyuridines (dU) in immunoglobulin (Ig) genes. Although AID has a strong preference for Ig genes, it can also target other genomic regions, giving rise to mutations or chromosomal translocations. Thus, understanding the specificity of AID has major implications for oncogenic transformation. However, approaching AID specificity has proved extremely challenging because AID deamination events occur at low frequencies. Here we have sequenced at very high depth >1500 genomic regions from GC B cells and identified 275 genes targeted by AID, including 30 of the previously known 35 AID targets. This has enabled for the first time to define the molecular features predictive of AID target specificity genome-wide. Furthermore, we identify the most highly mutated hotspot for AID activity described to date. We also find that Base Excision Repair (BER) and Mismatch Repair (MMR) systems, which are responsible for the resolution of AID deaminations, back-up each other to faithfully repair AID-induced lesions. Finally, our data establishes a novel link between AID mutagenic activity and malignant transformation. Overall design: Germinal center (CD19+FAS+GL7+) B cells were sorted from Peyer's patches of Ung+/-Msh2+/-, Ung+/-Msh2-/-, Ung-/-Msh2+/-, Ung-/-Msh2-/- and Aicda-/- mice. Genomic DNA was isolated, enriched with a custom SureSelect library of ~1600 RNA probes and deep sequenced. Four groups of mice were analzyed in 2 replicates; Aicda-/- mice were used as negative controls.