单核苷酸多态性（SNPs）、短串联重复序列和结构变异是造成C57BL/6和C57BL/10亚系间基因表达差异的原因。
SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains.
作者信息
Mortazavi Milad, Ren Yangsu, Saini Shubham, Antaki Danny, St Pierre Celine L, Williams April, Sohni Abhishek, Wilkinson Miles F, Gymrek Melissa, Sebat Jonathan, Palmer Abraham A
机构信息
Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
出版信息
Cell Genom. 2022 Mar 9;2(3). doi: 10.1016/j.xgen.2022.100102.
Mouse substrains are an invaluable model for understanding disease. We compared C57BL/6J, which is the most commonly used inbred mouse strain, with eight C57BL/6 and five C57BL/10 closely related inbred substrains. Whole-genome sequencing and RNA-sequencing analysis yielded 352,631 SNPs, 109,096 indels, 150,344 short tandem repeats (STRs), 3,425 structural variants (SVs), and 2,826 differentially expressed genes (DE genes) among these 14 strains; 312,981 SNPs (89%) distinguished the B6 and B10 lineages. These SNPs were clustered into 28 short segments that are likely due to introgressed haplotypes rather than new mutations. Outside of these introgressed regions, we identified 53 SVs, protein-truncating SNPs, and frameshifting indels that were associated with DE genes. Our results can be used for both forward and reverse genetic approaches and illustrate how introgression and mutational processes give rise to differences among these widely used inbred substrains.
小鼠亚系是理解疾病的宝贵模型。我们将最常用的近交小鼠品系C57BL/6J与8个C57BL/6和5个C57BL/10密切相关的近交亚系进行了比较。全基因组测序和RNA测序分析在这14个品系中产生了352,631个单核苷酸多态性（SNP）、109,096个插入缺失、150,344个短串联重复序列（STR）、3,425个结构变异（SV）和2,826个差异表达基因（DE基因）；312,981个SNP（89%）区分了B6和B10谱系。这些SNP聚集成28个短片段，这可能是由于渗入的单倍型而非新突变所致。在这些渗入区域之外，我们鉴定出53个与DE基因相关的SV、蛋白质截短SNP和移码插入缺失。我们的结果可用于正向和反向遗传方法，并阐明渗入和突变过程如何导致这些广泛使用的近交亚系之间的差异。
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