Dowell Robin, Odell Aaron, Richmond Phillip, Malmer Daniel, Halper-Stromberg Eitan, Bennett Beth, Larson Colin, Leach Sonia, Radcliffe Richard A
BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80309, USA.
Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA.
Mamm Genome. 2016 Dec;27(11-12):574-586. doi: 10.1007/s00335-016-9663-6. Epub 2016 Sep 20.
The Inbred Long- and Short-Sleep (ILS, ISS) mouse lines were selected for differences in acute ethanol sensitivity using the loss of righting response (LORR) as the selection trait. The lines show an over tenfold difference in LORR and, along with a recombinant inbred panel derived from them (the LXS), have been widely used to dissect the genetic underpinnings of acute ethanol sensitivity. Here we have sequenced the genomes of the ILS and ISS to investigate the DNA variants that contribute to their sensitivity difference. We identified ~2.7 million high-confidence SNPs and small indels and ~7000 structural variants between the lines; variants were found to occur in 6382 annotated genes. Using a hidden Markov model, we were able to reconstruct the genome-wide ancestry patterns of the eight inbred progenitor strains from which the ILS and ISS were derived, and found that quantitative trait loci that have been mapped for LORR were slightly enriched for DNA variants. Finally, by mapping and quantifying RNA-seq reads from the ILS and ISS to their strain-specific genomes rather than to the reference genome, we found a substantial improvement in a differential expression analysis between the lines. This work will help in identifying and characterizing the DNA sequence variants that contribute to the difference in ethanol sensitivity between the ILS and ISS and will also aid in accurate quantification of RNA-seq data generated from the LXS RIs.
近交长睡眠和短睡眠（ILS，ISS）小鼠品系是通过使用翻正反射消失（LORR）作为选择性状，根据急性乙醇敏感性差异选育出来的。这两个品系在LORR方面表现出超过十倍的差异，并且与从它们衍生而来的重组近交系面板（LXS）一起，被广泛用于剖析急性乙醇敏感性的遗传基础。在此，我们对ILS和ISS的基因组进行了测序，以研究导致它们敏感性差异的DNA变异。我们在这两个品系之间鉴定出约270万个高可信度单核苷酸多态性（SNP）和小插入缺失以及约7000个结构变异；发现这些变异存在于6382个注释基因中。使用隐马尔可夫模型，我们能够重建ILS和ISS所源自的八个近交祖系的全基因组祖先模式，并发现已定位到LORR的数量性状位点在DNA变异方面略有富集。最后，通过将来自ILS和ISS的RNA测序读数映射并定量到它们的品系特异性基因组而非参考基因组，我们发现在这两个品系之间的差异表达分析中有显著改进。这项工作将有助于识别和表征导致ILS和ISS之间乙醇敏感性差异的DNA序列变异，也将有助于准确量化从LXS重组近交系产生的RNA测序数据。
