Ustyantsev K V, Berezikov E V
Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
Vavilovskii Zhurnal Genet Selektsii. 2021 Feb;25(1):101-107. doi: 10.18699/VJ21.012.
In eukaryotes, trans-splicing is a process of nuclear pre-mRNA maturation where two different RNA molecules are joined together by the spliceosomal machinery utilizing mechanisms similar to cis-splicing. In diverse taxa of lower eukaryotes, spliced leader (SL) trans-splicing is the most frequent type of trans-splicing, when the same sequence derived from short small nuclear RNA molecules, called SL RNAs, is attached to the 5' ends of different non-processed pre-mRNAs. One of the functions of SL trans-splicing is processing polycistronic pre-mRNA molecules transcribed from operons, when several genes are transcribed as one pre-mRNA molecule. However, only a fraction of trans-spliced genes reside in operons, suggesting that SL trans-splicing must also have some other, less understood functions. Regenerative flatworms are informative model organisms which hold the keys to understand the mechanism of stem cell regulation and specialization during regeneration and homeostasis. Their ability to regenerate is fueled by the division and differentiation of the adult somatic stem cell population called neoblasts. Macrostomum lignano is a flatworm model organism where substantial technological advances have been achieved in recent years, including the development of transgenesis. Although a large fraction of genes in M. lignano were estimated to be SL trans-spliced, SL trans-splicing was not studied in detail in M. lignano before. Here, we performed the first comprehensive study of SL trans-splicing in M. lignano. By reanalyzing the existing genome and transcriptome data of M. lignano, we estimate that 30 % of its genes are SL trans-spliced, 15 % are organized in operons, and almost 40 % are both SL trans-spliced and in operons. We annotated and characterized the sequence of SL RNA and characterized conserved cis- and SL transsplicing motifs. Finally, we found that a majority of SL trans-spliced genes are evolutionarily conserved and significantly over-represented in neoblast-specific genes. Our findings suggest an important role of SL trans-splicing in the regulation and maintenance of neoblasts in M. lignano.
在真核生物中，反式剪接是核内前体mRNA成熟的一个过程，在此过程中，两个不同的RNA分子通过剪接体机制连接在一起，其利用的机制类似于顺式剪接。在低等真核生物的不同分类群中，剪接前导序列（SL）反式剪接是最常见的反式剪接类型，此时来自短的小核RNA分子（称为SL RNA）的相同序列会连接到不同的未加工前体mRNA的5'末端。SL反式剪接的功能之一是处理从操纵子转录而来的多顺反子前体mRNA分子，即几个基因作为一个前体mRNA分子进行转录。然而，只有一小部分反式剪接基因存在于操纵子中，这表明SL反式剪接必定还具有其他一些尚未完全了解的功能。再生扁虫是有价值的模式生物，对于理解再生和体内平衡过程中干细胞调控及特化机制至关重要。它们的再生能力由称为新细胞的成体体细胞干细胞群体的分裂和分化提供动力。利氏大口涡虫是一种扁虫模式生物，近年来在技术方面取得了重大进展，包括转基因技术的发展。尽管据估计利氏大口涡虫中很大一部分基因是SL反式剪接的，但此前在利氏大口涡虫中尚未对SL反式剪接进行详细研究。在此，我们首次对利氏大口涡虫中的SL反式剪接进行了全面研究。通过重新分析利氏大口涡虫现有的基因组和转录组数据，我们估计其30%的基因是SL反式剪接的，15%的基因组织成操纵子，近40%的基因既是SL反式剪接的又存在于操纵子中。我们对SL RNA的序列进行了注释和特征分析，并鉴定了保守的顺式和SL反式剪接基序。最后，我们发现大多数SL反式剪接基因在进化上是保守的，并且在新细胞特异性基因中显著富集。我们的研究结果表明SL反式剪接在利氏大口涡虫新细胞的调控和维持中起着重要作用。
