Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans
Abstract 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...
| Main Author: | |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2020-10-01
|
| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-020-03818-6 |
| _version_ | 1828401102428569600 |
|---|---|
| author | Meng Li |
| author_facet | Meng Li |
| author_sort | Meng Li |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-10T09:41:29Z |
| format | Article |
| id | doaj.art-985ce505ea0643d38fa33894a07cb331 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-10T09:41:29Z |
| publishDate | 2020-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-985ce505ea0643d38fa33894a07cb3312022-12-22T01:53:59ZengBMCBMC Bioinformatics1471-21052020-10-0121111510.1186/s12859-020-03818-6Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humansMeng Li0CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesAbstract 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.http://link.springer.com/article/10.1186/s12859-020-03818-6SplicingIntron splicing orderMost likely orderBayesian network |
| spellingShingle | Meng Li Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans BMC Bioinformatics Splicing Intron splicing order Most likely order Bayesian network |
| 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 | Splicing Intron splicing order Most likely order Bayesian network |
| url | http://link.springer.com/article/10.1186/s12859-020-03818-6 |
| work_keys_str_mv | AT mengli calculatingthemostlikelyintronsplicingordersinspombefruitflyarabidopsisthalianaandhumans |