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Interplays between cis- and trans-Acting Factors for Alternative Splicing in Response to Environmental Changes during Biological Invasions of Ascidians
Alternative splicing (AS), a pivotal biological process contributing to phenotypic plasticity, creates a bridge linking genotypes with phenotypes. Despite its importance, the AS mechanisms underlying environmental response and adaptation have not been well studied, and more importantly, the cis- and...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10573349/ https://www.ncbi.nlm.nih.gov/pubmed/37834365 http://dx.doi.org/10.3390/ijms241914921 |
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author | Huang, Xuena Li, Hanxi Zhan, Aibin |
author_facet | Huang, Xuena Li, Hanxi Zhan, Aibin |
author_sort | Huang, Xuena |
collection | PubMed |
description | Alternative splicing (AS), a pivotal biological process contributing to phenotypic plasticity, creates a bridge linking genotypes with phenotypes. Despite its importance, the AS mechanisms underlying environmental response and adaptation have not been well studied, and more importantly, the cis- and trans-acting factors influencing AS variation remain unclear. Using the model invasive congeneric ascidians, Ciona robusta, and Ciona savignyi, we compared their AS responses to environmental changes and explored the potential determinants. Our findings unveiled swift and dynamic AS changes in response to environmental challenges, and differentially alternative spliced genes (DASGs) were functionally enriched in transmembrane transport processes. Interestingly, both the prevalence and level of AS in C. robusta were lower than those observed in C. savignyi. Furthermore, these two indices were higher under temperature stresses compared to salinity stresses in C. savignyi. All the observed patterns underscore the species-specific and environmental context-dependent AS responses to environmental challenges. The dissimilarities in genomic structure and exon/intron size distributions between these two species likely contributed to the observed AS variation. Moreover, we identified a total of 11 and 9 serine/arginine-rich splicing factors (SRSFs) with conserved domains and gene structures in the genomes of C. robusta and C. savignyi, respectively. Intriguingly, our analysis revealed that all detected SRSFs did not exhibit prevalent AS regulations. Instead, we observed AS control over a set of genes related to splicing factors and spliceosome components. Altogether, our results elucidate species-specific and environmental challenge-dependent AS response patterns in closely related invasive ascidians. The identified splicing factors and spliceosome components under AS control offer promising candidates for further investigations into AS-mediated rapid responses to environmental challenges complementary to SRSFs. |
format | Online Article Text |
id | pubmed-10573349 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-105733492023-10-14 Interplays between cis- and trans-Acting Factors for Alternative Splicing in Response to Environmental Changes during Biological Invasions of Ascidians Huang, Xuena Li, Hanxi Zhan, Aibin Int J Mol Sci Article Alternative splicing (AS), a pivotal biological process contributing to phenotypic plasticity, creates a bridge linking genotypes with phenotypes. Despite its importance, the AS mechanisms underlying environmental response and adaptation have not been well studied, and more importantly, the cis- and trans-acting factors influencing AS variation remain unclear. Using the model invasive congeneric ascidians, Ciona robusta, and Ciona savignyi, we compared their AS responses to environmental changes and explored the potential determinants. Our findings unveiled swift and dynamic AS changes in response to environmental challenges, and differentially alternative spliced genes (DASGs) were functionally enriched in transmembrane transport processes. Interestingly, both the prevalence and level of AS in C. robusta were lower than those observed in C. savignyi. Furthermore, these two indices were higher under temperature stresses compared to salinity stresses in C. savignyi. All the observed patterns underscore the species-specific and environmental context-dependent AS responses to environmental challenges. The dissimilarities in genomic structure and exon/intron size distributions between these two species likely contributed to the observed AS variation. Moreover, we identified a total of 11 and 9 serine/arginine-rich splicing factors (SRSFs) with conserved domains and gene structures in the genomes of C. robusta and C. savignyi, respectively. Intriguingly, our analysis revealed that all detected SRSFs did not exhibit prevalent AS regulations. Instead, we observed AS control over a set of genes related to splicing factors and spliceosome components. Altogether, our results elucidate species-specific and environmental challenge-dependent AS response patterns in closely related invasive ascidians. The identified splicing factors and spliceosome components under AS control offer promising candidates for further investigations into AS-mediated rapid responses to environmental challenges complementary to SRSFs. MDPI 2023-10-05 /pmc/articles/PMC10573349/ /pubmed/37834365 http://dx.doi.org/10.3390/ijms241914921 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Huang, Xuena Li, Hanxi Zhan, Aibin Interplays between cis- and trans-Acting Factors for Alternative Splicing in Response to Environmental Changes during Biological Invasions of Ascidians |
title | Interplays between cis- and trans-Acting Factors for Alternative Splicing in Response to Environmental Changes during Biological Invasions of Ascidians |
title_full | Interplays between cis- and trans-Acting Factors for Alternative Splicing in Response to Environmental Changes during Biological Invasions of Ascidians |
title_fullStr | Interplays between cis- and trans-Acting Factors for Alternative Splicing in Response to Environmental Changes during Biological Invasions of Ascidians |
title_full_unstemmed | Interplays between cis- and trans-Acting Factors for Alternative Splicing in Response to Environmental Changes during Biological Invasions of Ascidians |
title_short | Interplays between cis- and trans-Acting Factors for Alternative Splicing in Response to Environmental Changes during Biological Invasions of Ascidians |
title_sort | interplays between cis- and trans-acting factors for alternative splicing in response to environmental changes during biological invasions of ascidians |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10573349/ https://www.ncbi.nlm.nih.gov/pubmed/37834365 http://dx.doi.org/10.3390/ijms241914921 |
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