An Approach to Elucidate NBS1 Function in DNA Repair Using Frequent Nonsynonymous Polymorphism in Wild Medaka (Oryzias latipes) Populations

Abstract

Nbs1 is one of the genes responsible for Nijmegen breakage syndrome, which is marked with high radiosensitivity. In human NBS1 (hNBS1), Q185E polymorphism is known as the factor to cancer risks, although its DSB repair defect has not been addressed. Here we investigated the genetic variations in medaka (Oryzias latipes) wild populations, and found 40 nonsynonymous single nucleotide polymorphisms (SNPs) in medaka nbs1 (olnbs1) gene within 5 inbred strains. A mutation to histidine in Q170 residue in olNbs1, which corresponds to Q185 residue of hNBS1, was widely distributed in the closed colonies derived from the eastern Korean population of medaka. Overexpression of H170 type olNbs1 in medaka cultured cell lines resulted in the increased accumulation of olNbs1 at laser-induced DSB sites. Autophosphorylation of DNA-dependent protein kinase at T2609 was suppressed after the γ-ray irradiation, which was followed by prolonged formation of γ-H2AX foci and delayed DSB repair. These findings suggested that the nonsynonymous SNP (Q170H) in olnbs1, which induced DSB repair defects, is specifically distributed in the eastern Korean population of medaka. Furthermore, examination using the variation within wild populations might provide a novel method to characterize a driving force to spread the disease risk alleles.

Medaka Population Genome Structure and Demographic History Described via Genotyping-by-Sequencing

“…The lab stocks originated from geographically distinct populations in East Asia and have been maintained since 1985 (Shima et al 1985) as closed colonies in the Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa City (Figure 1). These lab stocks maintain the genetic diversity originating from their habitat (Katsumura et al 2014; Igarashi et al 2017) and show less diversity within populations than between populations (Katsumura et al 2009). Because of these characteristics, we considered that one individual sampled from the lab stock would be adequate to represent its originating population.…”

“…Wild medaka populations have been maintained in certain universities and research institutes as a bioresource (hereafter, wild lab stocks) with funding from the Japanese government since 1985 (Shima et al 1985). These populations consist of more than 100 local-wild populations that have various phenotypic traits (Watanabe-Asaka et al 2014; Igarashi et al 2017) and abundant genetic diversity (Kasahara et al 2007). Geographical features affect the population structure of organisms.…”

“…Once genetic polymorphisms related to phenotypic traits in medaka are detected, in vivo experiments, such as genome editing experiments (Ansai and Kinoshita 2014), can be conducted to understand the functions of the genetic variants (Shimmura et al 2017). Revealing the functional difference between alleles in wild populations allows us to infer the role of genetic polymorphisms in human homologous genes (Igarashi et al 2017; Shimmura et al 2017).…”

Intraspecific diversity based on low temperature induced arrhythmia in embryonic heart of medaka (Oryzias latipes)

“…A common ancestor of the medaka is estimated to have diverged from a sister lineage O. luzonensis , followed by a divergence between the continental (E.KOR and W.KOR) and Japanese populations 5.4–6.0 million years (Myr) ago (Takehena, 2003; Kasahara, 2007). The two Japanese populations (N.JPN and S.JPN) diverged 4–5 Myr ago (Watanabe, 2006; Kasahara, 2007; Katsumura, 2017). These medaka groups have over 80 wild populations with large genetic diversity and have been used for analyses of the functional differences of genetic polymorphisms (Matsumoto, 2009; Katsumura, 2014; Igarashi, 2017).…”

“…The two Japanese populations (N.JPN and S.JPN) diverged 4–5 Myr ago (Watanabe, 2006; Kasahara, 2007; Katsumura, 2017). These medaka groups have over 80 wild populations with large genetic diversity and have been used for analyses of the functional differences of genetic polymorphisms (Matsumoto, 2009; Katsumura, 2014; Igarashi, 2017).…”