A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA
Studies have shown that post-spliced introns promote cell survival when nutrients are scarce, and intron loss/gain can influence many stages of mRNA metabolism. However, few approaches are currently available to study the correlation between intron sequences and their corresponding mature mRNA seque...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1151172/full |
| _version_ | 1828004016021307392 |
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| author | Suling Bo Qiuying Sun Pengfei Ning Ningping Yuan Yujie Weng Ying Liang Huitao Wang Zhanyuan Lu Zhanyuan Lu Zhanyuan Lu Zhanyuan Lu Zhongxian Li Xiaoqing Zhao Xiaoqing Zhao Xiaoqing Zhao Xiaoqing Zhao |
| author_facet | Suling Bo Qiuying Sun Pengfei Ning Ningping Yuan Yujie Weng Ying Liang Huitao Wang Zhanyuan Lu Zhanyuan Lu Zhanyuan Lu Zhanyuan Lu Zhongxian Li Xiaoqing Zhao Xiaoqing Zhao Xiaoqing Zhao Xiaoqing Zhao |
| author_sort | Suling Bo |
| collection | DOAJ |
| description | Studies have shown that post-spliced introns promote cell survival when nutrients are scarce, and intron loss/gain can influence many stages of mRNA metabolism. However, few approaches are currently available to study the correlation between intron sequences and their corresponding mature mRNA sequences. Here, based on the results of the improved Smith-Waterman local alignment-based algorithm method (SW method) and binding free energy weighted local alignment algorithm method (BFE method), the optimal matched segments between introns and their corresponding mature mRNAs in Caenorhabditis elegans (C.elegans) and their relative matching frequency (RF) distributions were obtained. The results showed that although the distributions of relative matching frequencies on mRNAs obtained by the BFE method were similar to the SW method, the interaction intensity in 5’and 3’untranslated regions (UTRs) regions was weaker than the SW method. The RF distributions in the exon-exon junction regions were comparable, the effects of long and short introns on mRNA and on the five functional sites with BFE method were similar to the SW method. However, the interaction intensity in 5’and 3’UTR regions with BFE method was weaker than with SW method. Although the matching rate and length distribution shape of the optimal matched fragment were consistent with the SW method, an increase in length was observed. The matching rates and the length of the optimal matched fragments were mainly in the range of 60%–80% and 20-30bp, respectively. Although we found that there were still matching preferences in the 5’and 3’UTR regions of the mRNAs with BFE, the matching intensities were significantly lower than the matching intensities between introns and their corresponding mRNAs with SW method. Overall, our findings suggest that the interaction between introns and mRNAs results from synergism among different types of sequences during the evolutionary process. |
| first_indexed | 2024-04-10T07:08:56Z |
| format | Article |
| id | doaj.art-e9e14639131e4a408c7a3c28e2c624cb |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-10T07:08:56Z |
| publishDate | 2023-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-e9e14639131e4a408c7a3c28e2c624cb2023-02-27T04:57:04ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-02-011410.3389/fgene.2023.11511721151172A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNASuling Bo0Qiuying Sun1Pengfei Ning2Ningping Yuan3Yujie Weng4Ying Liang5Huitao Wang6Zhanyuan Lu7Zhanyuan Lu8Zhanyuan Lu9Zhanyuan Lu10Zhongxian Li11Xiaoqing Zhao12Xiaoqing Zhao13Xiaoqing Zhao14Xiaoqing Zhao15College of Computer Information, Inner Mongolia Medical University, Hohhot, ChinaDepartment of Oncology, Inner Mongolia Cancer Hospital and The Affiliated People’s Hospital of Inner Mongolia Medical University, Hohhot, ChinaCollege of Computer Information, Inner Mongolia Medical University, Hohhot, ChinaCollege of Computer Information, Inner Mongolia Medical University, Hohhot, ChinaCollege of Computer Information, Inner Mongolia Medical University, Hohhot, ChinaCollege of Computer Information, Inner Mongolia Medical University, Hohhot, ChinaCollege of Computer Information, Inner Mongolia Medical University, Hohhot, ChinaInner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaSchool of Life Science, Inner Mongolia University, Hohhot, ChinaKey Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, ChinaInner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, ChinaCollege of Computer Information, Inner Mongolia Medical University, Hohhot, ChinaInner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaSchool of Life Science, Inner Mongolia University, Hohhot, ChinaKey Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, ChinaInner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, ChinaStudies have shown that post-spliced introns promote cell survival when nutrients are scarce, and intron loss/gain can influence many stages of mRNA metabolism. However, few approaches are currently available to study the correlation between intron sequences and their corresponding mature mRNA sequences. Here, based on the results of the improved Smith-Waterman local alignment-based algorithm method (SW method) and binding free energy weighted local alignment algorithm method (BFE method), the optimal matched segments between introns and their corresponding mature mRNAs in Caenorhabditis elegans (C.elegans) and their relative matching frequency (RF) distributions were obtained. The results showed that although the distributions of relative matching frequencies on mRNAs obtained by the BFE method were similar to the SW method, the interaction intensity in 5’and 3’untranslated regions (UTRs) regions was weaker than the SW method. The RF distributions in the exon-exon junction regions were comparable, the effects of long and short introns on mRNA and on the five functional sites with BFE method were similar to the SW method. However, the interaction intensity in 5’and 3’UTR regions with BFE method was weaker than with SW method. Although the matching rate and length distribution shape of the optimal matched fragment were consistent with the SW method, an increase in length was observed. The matching rates and the length of the optimal matched fragments were mainly in the range of 60%–80% and 20-30bp, respectively. Although we found that there were still matching preferences in the 5’and 3’UTR regions of the mRNAs with BFE, the matching intensities were significantly lower than the matching intensities between introns and their corresponding mRNAs with SW method. Overall, our findings suggest that the interaction between introns and mRNAs results from synergism among different types of sequences during the evolutionary process.https://www.frontiersin.org/articles/10.3389/fgene.2023.1151172/fullintronalignment methodinteractionmRNAevolutionary process |
| spellingShingle | Suling Bo Qiuying Sun Pengfei Ning Ningping Yuan Yujie Weng Ying Liang Huitao Wang Zhanyuan Lu Zhanyuan Lu Zhanyuan Lu Zhanyuan Lu Zhongxian Li Xiaoqing Zhao Xiaoqing Zhao Xiaoqing Zhao Xiaoqing Zhao A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA Frontiers in Genetics intron alignment method interaction mRNA evolutionary process |
| title | A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA |
| title_full | A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA |
| title_fullStr | A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA |
| title_full_unstemmed | A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA |
| title_short | A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA |
| title_sort | novel approach to analyze the association characteristics between post spliced introns and their corresponding mrna |
| topic | intron alignment method interaction mRNA evolutionary process |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1151172/full |
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