Homozygous mutation of the RNA kinase CLP1 (cleavage factor polyribonucleotide kinase subunit 1) causes pontocerebellar hypoplasia type 10 (PCH10), a pediatric neurodegenerative disease. CLP1 is associated with the transfer RNA (tRNA) splicing endonuclease complex and the cleavage and polyadenylation machinery, but its function remains unclear. We generated two mouse models of PCH10: one homozygous for the disease-associated Clp1 mutation, R140H, and one heterozygous for this mutation and a null allele. Both models exhibit loss of lower motor neurons and neurons of the deep cerebellar nuclei. To explore whether Clp1 mutation impacts tRNA splicing, we profiled the products of intron-containing tRNA genes. While mature tRNAs were expressed at normal levels in mutant mice, numerous other products of intron-containing tRNA genes were dysregulated, with pre-tRNAs, introns, and certain tRNA fragments up-regulated, and other fragments down-regulated. However, the spatiotemporal patterns of dysregulation do not correlate with pathogenicity for most altered tRNA products. To elucidate the effect of Clp1 mutation on precursor messenger RNA (pre-mRNA) cleavage, we analyzed poly(A) site (PAS) usage and gene expression in Clp1^R140H/− spinal cord. PAS usage was shifted from proximal to distal sites in the mutant mouse, particularly in short and closely spaced genes. Many such genes were also expressed at lower levels in the Clp1^R140H/− mouse, possibly as a result of impaired transcript maturation. These findings are consistent with the hypothesis that select genes are particularly dependent upon CLP1 for proper pre-mRNA cleavage, suggesting that impaired mRNA 3′ processing may contribute to pathogenesis in PCH10.

RNA 激酶CLP1（切割因子多核糖核苷酸激酶亚基 1）的纯合突变导致 10 型脑桥小脑发育不全 (PCH10)，这是一种儿科神经退行性疾病。CLP1 与转移 RNA (tRNA) 剪接核酸内切酶复合物以及切割和多聚腺苷酸化机制有关，但其功能尚不清楚。我们生成了两种 PCH10 小鼠模型：一种是与疾病相关的Clp1突变 R140H 的纯合子，另一种是该突变和无效等位基因的杂合子。两种模型都表现出下运动神经元和小脑深部核神经元的损失。探讨Clp1是否突变影响 tRNA 剪接，我们分析了含有内含子的 tRNA 基因的产物。虽然成熟的 tRNA 在突变小鼠中以正常水平表达，但包含内含子的 tRNA 基因的许多其他产物失调，前 tRNA、内含子和某些 tRNA 片段上调，而其他片段下调。然而，失调的时空模式与大多数改变的 tRNA 产物的致病性无关。为了阐明Clp1突变对前体信使 RNA（pre-mRNA）切割的影响，我们分析了Clp1 ^{R140H/− 中}poly（A）位点（PAS）的使用和基因表达脊髓。PAS 的使用在突变小鼠中从近端位点转移到远端位点，特别是在短且间隔很近的基因中。许多这样的基因也在Clp1 ^R140H/-小鼠中以较低水平表达，可能是转录成熟受损的结果。这些发现与选择基因特别依赖 CLP1 进行适当的前 mRNA 切割的假设一致，这表明受损的 mRNA 3' 加工可能有助于 PCH10 的发病机制。