Predominant contribution of cis-regulatory divergence in the evolution of mouse alternative splicing. Predominant cis-contribution in mouse AS evolution

Divergence of alternative splicing represents one of the major driving forces to shape phenotypic diversity during evolution. However, the extent to which these divergences could be explained by the evolving cis-regulatory versus trans-acting factors remains unresolved. To globally investigate the relative contributions of the two factors for the first time in mammals, we measured splicing difference between C57BL/6J and SPRET/EiJ mouse strains and allele-specific splicing pattern in their F1 hybrid. Out of 11,818 alternative splicing events expressed in the cultured fibroblast cells, we identified 796 with significant difference between the parental strains. After integrating allele-specific data from F1 hybrid, we demonstrated that these events could be predominately attributed to cis-regulatory variants, including those residing at and beyond canonical splicing sites. Contrary to previous observations in Drosophila, such predominant contribution was consistently observed across different types of alternative splicing. Further analysis of liver tissues from the same mouse strains and re-analysis of published datasets on other strains showed similar trends, implying in general the predominant contribution of cis-regulatory changes in the evolution of mouse alternative splicing.

可变剪接（alternative splicing）的分化是演化过程中塑造表型多样性的主要驱动力之一。然而，此类剪接分化在多大程度上可由不断演化的顺式调控（cis-regulatory）与反式作用（trans-acting）因子解释，目前仍未得到明确解答。为首次在哺乳动物中全局探究这两类因子的相对贡献，我们检测了C57BL/6J与SPRET/EiJ两种小鼠品系间的剪接差异，以及它们的F1杂交后代（F1 hybrid）中的等位基因特异性剪接（allele-specific splicing）模式。在培养的成纤维细胞中表达的11818个可变剪接事件中，我们鉴定出796个在亲本品系间存在显著差异的事件。整合F1杂交后代的等位基因特异性剪接数据后，我们证实这些事件主要可归因于顺式调控变异，包括位于经典剪接位点及之外区域的变异。与此前在果蝇（Drosophila）中的研究发现相反，这种主导贡献在各类可变剪接类型中均一致存在。对同一小鼠品系肝脏组织的进一步分析，以及对其他品系已发表数据集的重新分析均呈现相似趋势，这表明在小鼠可变剪接的演化过程中，顺式调控变化普遍占据主导贡献。