Eukaryotic genes are interrupted by introns that must be accurately spliced from mRNA precursors. With an average length of 25 nt, the more than 90,000 introns of Paramecium tetraurelia stand among the shortest introns reported in eukaryotes. The mechanisms specifying the correct recognition of these tiny introns remain poorly understood. Splicing can occur cotranscriptionally, and it has been proposed that chromatin structure might influence splice site recognition. To investigate the roles of nucleosome positioning in intron recognition, we determined the nucleosome occupancy along the P. tetraurelia genome. We show that P. tetraurelia displays a regular nucleosome array with a nucleosome repeat length of ∼151 bp, among the smallest periodicities reported. Our analysis has revealed that introns are frequently associated with inter-nucleosomal DNA, pointing to an evolutionary constraint favoring introns at the AT-rich nucleosome edge sequences. Using accurate splicing efficiency data from cells depleted for nonsense-mediated decay effectors, we show that introns located at the edge of nucleosomes display higher splicing efficiency than those at the center. However, multiple regression analysis indicates that the low GC content of introns, rather than nucleosome positioning, is associated with high splicing efficiency. Our data reveal a complex link between GC content, nucleosome positioning, and intron evolution in Paramecium.

中文翻译：

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GC 含量，但不是核小体定位，直接影响草履虫的内含子剪接效率

真核基因被必须从 mRNA 前体准确剪接的内含子打断。草履虫的平均长度为 25 nt，超过 90,000 个内含子是真核生物中报道的最短内含子之一。指定正确识别这些微小内含子的机制仍然知之甚少。剪接可以共转录发生，并且已经提出染色质结构可能影响剪接位点识别。为了研究核小体定位在内含子识别中的作用，我们确定了沿P. tetraurelia基因组的核小体占据。我们证明了P. tetraurelia显示了一个规则的核小体阵列，其核小体重复长度约为 151 bp，是报告的最小周期性之一。我们的分析表明，内含子经常与核小体间 DNA 相关，这表明在富含 AT 的核小体边缘序列中存在有利于内含子的进化限制。使用来自无义介导的衰变效应器耗尽的细胞的准确剪接效率数据，我们表明位于核小体边缘的内含子比位于中心的内含子显示出更高的剪接效率。然而，多元回归分析表明，内含子的低 GC 含量，而不是核小体的定位，与高剪接效率有关。我们的数据揭示了草履虫中 GC 含量、核小体定位和内含子进化之间的复杂联系。