| 引用本文: | 张强,赵小庆,薄素玲,曹艳娟,苏文霞.mRNA序列与相应内含子序列匹配的普适性分析[J].生物信息学,2020,18(3):149-156. |
| ZHANG Qiang,ZHAO Xiaoqing,BO Suling,CAO Yanjuan,SU Wenxia.Conservative analysis on matching between mRNA and corresponding intron[J].Chinese Journal of Bioinformatics,2020,18(3):149-156. |
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| 摘要: |
| 剪切后的内含子在基因表达和调控过程中发挥重要作用,由此在成熟mRNA与相应的内含子之间也存在相互作用,并且二者协同进化。为了验证这一理论,以13个物种的基因组作为研究样本,凭借Smith-Waterman的局域比对方法,最终得到在成熟mRNA与其内含子序列之间的最佳匹配片段,同时在mRNA序列上显示出最佳匹配强度的分布区。然后对最佳匹配片段的长度、配对率的分布这两项参数进行分析之后,发现最佳匹配片段的这两个参数的特征,与siRNA和miRNA的结合特征是相近的；在mRNA序列上,得出UTR区与内含子相互作用强,GC含量低的片段偏好结合到3’UTR区,相反GC含量高的片段更倾向与5’UTR区发生相互作用。因此,最佳匹配片段的序列特征符合RNA-RNA相互作用规律,可以把内含子看成是一种具有基因表达调控功能的序列。以上研究对于进一步探讨内含子的功能和进化具有重大意义。 |
| 关键词: mRNA序列 内含子 局域比对 最佳匹配片段 GC含量 |
| DOI：10.12113/201911004 |
| 分类号:Q61 |
| 文献标识码:A |
| 基金项目:内蒙古农业大学博士科研启动基金(No.NDYB2016-13);国家自然科学基金(No.11747084);内蒙古自然科学基金(No.2018BS03001)和内蒙古农业大学基础学科科研启动基金(No.JC2017003). |
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| Conservative analysis on matching between mRNA and corresponding intron |
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ZHANG Qiang1, ZHAO Xiaoqing3, BO Suling2, CAO Yanjuan1, SU Wenxia1
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(1.College of Science, Inner Mongolia Agriculture University, Hohhot 010018, China;2.College of Computer and Information Inner Mongolia Medical University, Hohhot 010110, China; 3.Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Huhhot 010031, China)
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| Abstract: |
| Introns after splicing play an important role in expression and regulation. Therefore, it is found that there is interaction between mature mRNA and its corresponding intron, and the relation is coevolution. In order to verify this theory, the genome sequences of 13 species were taken as research objects, and the optimal matched segments between mature mRNA and its intron sequences were obtained by using the local matching method named Smith-Waterman. Meanwhile, the distribution of the optimal matched segments on mRNA was obtained. Analysis results show that the average length and matching rate distribution of the optimal matched segments were similar to the combined characteristics of siRNA and miRNA. The UTR regions on mRNA had strong interaction with introns. Segments with low GC content were more likely to interact with 3’UTR region, while those with high GC content were prone to interact with 5’UTR region. Hence, the sequence characteristics of the optimal matched segments are coincident with the general regulation of RNA-RNA interaction, and introns can be regarded as functional segments of regulating gene expression. The conclusion is of constructive significance for further study the function and evolution of introns. |
| Key words: mRNA Intron Local alignment Optimal matched segments GC content |
