Identification of 129S6/SvEvTac-Specific Polymorphisms on Mouse Chromosome 11

Abstract

Polymorphisms such as single-nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) can be associated with phenotypic traits and be used as markers for disease diagnosis. Identification of these genetic variations within laboratory mice is crucial to improve our understanding of the genetic background of the mice used for research. As part of a positional cloning project, we sequenced six genes (Mettl16, Evi2a, Psmd11, Cct6d, Rffl, and Ap2b1) within a 6.8-Mb domain of mmu chr 11 in the C57BL/6J and 129S6/SvEvTac inbred strains. Although 129S6/SvEvTac is widely used in the mouse community, there is very little current (or projected future) sequence information available for this strain. We identified 6 Indels and 21 novel SNPs and confirmed genotype information for 114 additional SNPs in these 6 genes. Mettl16 and Ap2b1 contained the largest numbers of variants between the C57BL/6J and 129S6/SvEvTac strains. In addition, we found five new SNPs between 129S6/SvEvTac and 129S1/SvImJ within the Ap2b1 locus. Although we did not detect differences between C57BL/6J and 129S6/SvEvTac within Evi2a, this locus contains a relatively high SNP density compared with the surrounding sequence. Our study highlights the genetic differences among three inbred mouse strains (C57BL/6J, 129S6/SvEvTac, and 129S1/SvImJ) and provides valuable sequence information that can be used to track alleles in genomics-based studies.

ENU mutagenesis reveals that Notchless homolog 1 (Drosophila) affects Cdkn1a and several members of the Wnt pathway during murine pre-implantation development

“…We found no non-synonymous mutations in our first 7 candidates ( Ap2b1 , Cct6b, Suz12, Rffl, Evi2a, Psmd11 or Taf15 ) [38] . However, we identified a T 1184 G transversion (I 395 S missense mutation) in l11Jus1 heterozygotes in exon 10 of Nle1 (Figure 1D).…”

Identification of methylation‐driven genes related to prognosis in clear‐cell renal cell carcinoma

“…The lower the methylation level of the other three genes EVI2A, C11orf21, and SSX1, the worse the survival, and the combined survival analysis uncovered that the patients with low methylated/ high expression had worse prognosis than those with high methylated/low expression. EVI2A is a protein-coding gene that can be employed to diagnose diseases (Lo, Shen, Baumgarner, Cramer, & Lossie, 2012). In addition, some studies have revealed that it is also a specific tumor suppressor factor of lymphocytes (X.-W. Li et al, 2014), and the upregulation of EVI2A gene expression may increase the malignant risk of malignant peripheral schwannoma (MPNST; Pasmant et al, 2011).…”