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Summary: Somatic hypermutation (SHM) introduces point mutations into immunoglobulin (Ig) genes but also causes mutations in other parts of the genome. We have used lentiviral SHM reporter vectors to identify regions of the genome that are susceptible (“hot”) and resistant (“cold”) to SHM, revealing that SHM susceptibility and resistance are often properties of entire topologically associated domains (TADs). Comparison of hot and cold TADs reveals that while levels of transcription are equivalent, hot TADs are enriched for the cohesin loader NIPBL, super-enhancers, markers of paused/stalled RNA polymerase 2, and multiple important B cell transcription factors. We demonstrate that at least some hot TADs contain enhancers that possess SHM targeting activity and that insertion of a strong Ig SHM-targeting element into a cold TAD renders it hot. Our findings lead to a model for SHM susceptibility involving the cooperative action of cis-acting SHM targeting elements and the dynamic and architectural properties of TADs. : Senigl et al. show that genome susceptibility to somatic hypermutation (SHM) is confined within topologically associated domains (TADs) and is linked to markers of strong enhancers and stalled transcription and high levels of the cohesin loader NIPBL. Insertion of an ectopic SHM targeting element renders an entire TAD susceptible to SHM. Keywords: somatic hypermutation, activation induced deaminase, topologically associated domain, chromatin structure, chromatin loop extrusion, transcription factor

Simian virus 40 (SV40) is a monkey virus with tumorigenic potential in rodents and is associated with several types of human cancers, including lymphomas. A related Merkel cell polyomavirus causes carcinoma in humans by expressing truncated large tumor antigen (LT), with truncations caused by APOBEC family of cytidine deaminase-induced mutations. AID (activation-induced cytidine deaminase), a member of the APOBEC family, is the initiator of the antibody diversification process known as somatic hypermutation and its aberrant expression and targeting is a frequent source of lymphomagenesis. In this study, we investigated whether AID could cause mutations in SV40 LT. We demonstrate that the SV40 enhancer has strong somatic hypermutation targeting activity in several cell types and that AID-induced mutations accumulate in SV40 LT in B cells and kidney cells and cause truncated LT expression in B cells. Our results argue that the ability of the SV40 enhancer to target somatic hypermutation to LT is a potential source of LT truncation events that could contribute to tumorigenesis in various cell types, thereby linking SV40 infection with malignant development through a novel mutagenic pathway.

Longevity-related genes have been found in humans, mice, dogs and in several other animal species. The goal of this study was to perform genetic analysis of long-lived European bisons with the aim to find genes that are associated with longevity using GWAS and further sequencing of a wider sample panel. European bison has a unique history of near extinction and the recovery of the species from just a few founder individuals. Together with the short medium lifespan, the expected genetic homogeneity makes bison a suitable model for studying longevity. Particular single nucleotide polymorphisms within three genes, BCKDHB, FER1L6 and SERPINI2, were found significantly overrepresented in long-lived European bisons. In SERPINI2, the longevity-associated single nucleotide polymorphism localizes to an exon. In the protein encoded by the SERPINI2 gene, amino acid leucine present in the reference European bisons is replaced by tryptophan in the long-lived animals. This study is the first to determine longevity-associated variants in genes in European bison. Association of the FER1L6 gene with longevity shows a possible sex dependency.