Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Bo, Suling, Sun, Qiuying, Ning, Pengfei, Yuan, Ningping, Weng, Yujie, Liang, Ying, Wang, Huitao, Lu, Zhanyuan, Li, Zhongxian, Zhao, Xiaoqing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
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
_version_ 1784905853557538816
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
work_keys_str_mv AT bosuling anovelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT sunqiuying anovelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT ningpengfei anovelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT yuanningping anovelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT wengyujie anovelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT liangying anovelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT wanghuitao anovelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT luzhanyuan anovelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT lizhongxian anovelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT zhaoxiaoqing anovelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT bosuling novelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT sunqiuying novelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT ningpengfei novelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT yuanningping novelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT wengyujie novelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT liangying novelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT wanghuitao novelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT luzhanyuan novelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT lizhongxian novelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna
AT zhaoxiaoqing novelapproachtoanalyzetheassociationcharacteristicsbetweenpostsplicedintronsandtheircorrespondingmrna