Translational efficiency is subject to extensive regulation. However, the factors influencing such regulation are poorly understood. In Caenorhabditis elegans, 62% of genes are trans-spliced to a specific spliced leader (SL1), which replaces part of the native 5′ untranslated region (5′ UTR). Given the pivotal role the 5′ UTR plays in the regulation of translational efficiency, we hypothesized that SL1 trans-splicing functions to regulate translational efficiency. With genome-wide analysis on Ribo-seq data, polysome profiling experiments, and CRISPR-Cas9–based genetic manipulation of trans-splicing sites, we found four lines of evidence in support of this hypothesis. First, SL1 trans-spliced genes have higher translational efficiencies than non-trans-spliced genes. Second, SL1 trans-spliced genes have higher translational efficiencies than non-trans-spliced orthologous genes in other nematode species. Third, an SL1 trans-spliced isoform has higher translational efficiency than the non-trans-spliced isoform of the same gene. Fourth, deletion of trans-splicing sites of endogenous genes leads to reduced translational efficiency. Importantly, we demonstrated that SL1 trans-splicing plays a key role in enhancing translational efficiencies of essential genes. We further discovered that SL1 trans-splicing likely enhances translational efficiency by shortening the native 5′ UTRs, hence reducing the presence of upstream start codons (uAUG) and weakening mRNA secondary structures. Taken together, our study elucidates the global function of trans-splicing in enhancing translational efficiency in nematodes, paving the way for further understanding the genomic mechanisms of translational regulation.

翻译效率受到广泛的监管。但是，影响这种调节的因素知之甚少。在秀丽隐杆线虫，基因62％的反式剪接到一个特定的剪接前导（SL1），它取代了天然的5'非翻译区（5'UTR）的一部分。鉴于5'UTR中的翻译效率的调节起着举足轻重的作用，我们推测SL1反式剪接功能调节翻译效率。通过对Ribo-seq数据进行全基因组分析，多核糖体谱分析实验以及基于CRISPR-Cas9的反式剪接位点遗传操作，我们发现了四行证据支持这一假说。首先，SL1反剪接的基因具有比非更高翻译效率的反式剪接的基因。其次，SL1反式剪接的基因具有比非更高翻译效率反式拼接在其他线虫种类同源基因。第三，SL1反式叠接同种型具有比非更高翻译效率的反式同基因剪接同种型。第四，内源基因反式剪接位点的缺失导致翻译效率降低。重要的是，我们证明了SL1反式拼接在增强必需基因的翻译效率关键作用。我们进一步发现SL1反剪接可能通过缩短天然的5'UTR来提高翻译效率，从而减少了上游起始密码子（uAUG）的存在并削弱了mRNA的二级结构。总之，我们的研究阐明的全局函数反在提高线虫翻译效率拼接，从而为进一步理解转录调控的基因组机制的方式。