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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...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10008863/ https://www.ncbi.nlm.nih.gov/pubmed/36923795 http://dx.doi.org/10.3389/fgene.2023.1151172 |
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author | Bo, Suling Sun, Qiuying Ning, Pengfei Yuan, Ningping Weng, Yujie Liang, Ying Wang, Huitao Lu, Zhanyuan Li, Zhongxian Zhao, Xiaoqing |
author_facet | Bo, Suling Sun, Qiuying Ning, Pengfei Yuan, Ningping Weng, Yujie Liang, Ying Wang, Huitao Lu, Zhanyuan Li, Zhongxian Zhao, Xiaoqing |
author_sort | Bo, Suling |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-10008863 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-100088632023-03-14 A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA Bo, Suling Sun, Qiuying Ning, Pengfei Yuan, Ningping Weng, Yujie Liang, Ying Wang, Huitao Lu, Zhanyuan Li, Zhongxian Zhao, Xiaoqing Front Genet Genetics 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. Frontiers Media S.A. 2023-02-27 /pmc/articles/PMC10008863/ /pubmed/36923795 http://dx.doi.org/10.3389/fgene.2023.1151172 Text en Copyright © 2023 Bo, Sun, Ning, Yuan, Weng, Liang, Wang, Lu, Li and Zhao. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Bo, Suling Sun, Qiuying Ning, Pengfei Yuan, Ningping Weng, Yujie Liang, Ying Wang, Huitao Lu, Zhanyuan Li, Zhongxian Zhao, Xiaoqing A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA |
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 | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10008863/ https://www.ncbi.nlm.nih.gov/pubmed/36923795 http://dx.doi.org/10.3389/fgene.2023.1151172 |
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