Bo Suling, Sun Qiuying, Li Zhongxian, Aodun Gerile, Ji Yucheng, Wei Lihua, Wang Chao, Lu Zhanyuan, Zhang Qiang, Zhao Xiaoqing
College of Computer Information, Inner Mongolia Medical University, Hohhot, China.
Department of Oncology, Inner Mongolia Cancer Hospital and the Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, China.
Front Genet. 2023 Apr 12;14:1151703. doi: 10.3389/fgene.2023.1151703. eCollection 2023.
Introns, as important vectors of biological functions, can influence many stages of mRNA metabolism. However, in recent research, post-spliced introns are rarely considered. In this study, the optimal matched regions between introns and their mRNAs in nine model organism genomes were investigated with improved Smith-Waterman local alignment software. Our results showed that the distributions of mRNA optimal matched frequencies were highly consistent or universal. There are optimal matched frequency peaks in the UTR regions, which are obvious, especially in the 3'-UTR. The matched frequencies are relatively low in the CDS regions of the mRNA. The distributions of the optimal matched frequencies around the functional sites are also remarkably changed. The centers of the GC content distributions for different sequences are different. The matched rate distributions are highly consistent and are located mainly between 60% and 80%. The most probable value of the optimal matched segments is about 20 bp for lower eukaryotes and 30 bp for higher eukaryotes. These results show that there are abundant functional units in the introns, and these functional units are correlated structurally with all kinds of sequences of mRNA. The interaction between the post-spliced introns and their corresponding mRNAs may play a key role in gene expression.
内含子作为生物功能的重要载体，可影响mRNA代谢的多个阶段。然而，在最近的研究中，很少考虑剪接后的内含子。在本研究中，使用改进的Smith-Waterman局部比对软件研究了9种模式生物基因组中内含子与其mRNA之间的最佳匹配区域。我们的结果表明，mRNA最佳匹配频率的分布高度一致或具有普遍性。UTR区域存在明显的最佳匹配频率峰值，尤其是在3'-UTR中。mRNA的CDS区域中的匹配频率相对较低。功能位点周围的最佳匹配频率分布也有显著变化。不同序列的GC含量分布中心不同。匹配率分布高度一致，主要位于60%至80%之间。对于低等真核生物，最佳匹配片段的最可能值约为20bp，对于高等真核生物则为30bp。这些结果表明，内含子中存在丰富的功能单元，并且这些功能单元在结构上与mRNA的各种序列相关。剪接后的内含子与其相应mRNA之间的相互作用可能在基因表达中起关键作用。
