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Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans
BACKGROUND: Introns have been shown to be spliced in a defined order, and this order influences both alternative splicing regulation and splicing fidelity, but previous studies have only considered neighbouring introns. The detailed intron splicing order remains unknown. RESULTS: In this work, a met...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2020
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7585206/ https://www.ncbi.nlm.nih.gov/pubmed/33099301 http://dx.doi.org/10.1186/s12859-020-03818-6 |
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author | Li, Meng |
author_facet | Li, Meng |
author_sort | Li, Meng |
collection | PubMed |
description | BACKGROUND: Introns have been shown to be spliced in a defined order, and this order influences both alternative splicing regulation and splicing fidelity, but previous studies have only considered neighbouring introns. The detailed intron splicing order remains unknown. RESULTS: In this work, a method was developed that can calculate the intron splicing orders of all introns in each transcript. A simulation study showed that this method can accurately calculate intron splicing orders. I further applied this method to real S. pombe, fruit fly, Arabidopsis thaliana, and human sequencing datasets and found that intron splicing orders change from gene to gene and that humans contain more not in-order spliced transcripts than S. pombe, fruit fly and Arabidopsis thaliana. In addition, I reconfirmed that the first introns in humans are spliced slower than those in S. pombe, fruit fly, and Arabidopsis thaliana genome-widely. Both the calculated most likely orders and the method developed here are available on the web. CONCLUSIONS: A novel computational method was developed to calculate the intron splicing orders and applied the method to real sequencing datasets. I obtained intron splicing orders for hundreds or thousands of genes in four organisms. I found humans contain more number of not in-order spliced transcripts. |
format | Online Article Text |
id | pubmed-7585206 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-75852062020-10-26 Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans Li, Meng BMC Bioinformatics Methodology Article BACKGROUND: Introns have been shown to be spliced in a defined order, and this order influences both alternative splicing regulation and splicing fidelity, but previous studies have only considered neighbouring introns. The detailed intron splicing order remains unknown. RESULTS: In this work, a method was developed that can calculate the intron splicing orders of all introns in each transcript. A simulation study showed that this method can accurately calculate intron splicing orders. I further applied this method to real S. pombe, fruit fly, Arabidopsis thaliana, and human sequencing datasets and found that intron splicing orders change from gene to gene and that humans contain more not in-order spliced transcripts than S. pombe, fruit fly and Arabidopsis thaliana. In addition, I reconfirmed that the first introns in humans are spliced slower than those in S. pombe, fruit fly, and Arabidopsis thaliana genome-widely. Both the calculated most likely orders and the method developed here are available on the web. CONCLUSIONS: A novel computational method was developed to calculate the intron splicing orders and applied the method to real sequencing datasets. I obtained intron splicing orders for hundreds or thousands of genes in four organisms. I found humans contain more number of not in-order spliced transcripts. BioMed Central 2020-10-24 /pmc/articles/PMC7585206/ /pubmed/33099301 http://dx.doi.org/10.1186/s12859-020-03818-6 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Methodology Article Li, Meng Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans |
title | Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans |
title_full | Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans |
title_fullStr | Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans |
title_full_unstemmed | Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans |
title_short | Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans |
title_sort | calculating the most likely intron splicing orders in s. pombe, fruit fly, arabidopsis thaliana, and humans |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7585206/ https://www.ncbi.nlm.nih.gov/pubmed/33099301 http://dx.doi.org/10.1186/s12859-020-03818-6 |
work_keys_str_mv | AT limeng calculatingthemostlikelyintronsplicingordersinspombefruitflyarabidopsisthalianaandhumans |