Tissue-specific temperature dependence of RNA editing levels in zebrafish
Abstract Background RNA editing by adenosine deaminase acting on RNA (ADAR) occurs in all metazoans and fulfils several functions. Here, we examined effects of acclimation temperature (27 °C, 18 °C,13 °C) on editing patterns in six tissues of zebrafish (Danio rerio). Results Sites and total amounts...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-11-01
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| Series: | BMC Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12915-023-01738-4 |
| _version_ | 1797451503596732416 |
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| author | Wenhao Li Mengdi Bu Ruiqin Hu Shouwen Jiang Liangbiao Chen George N. Somero |
| author_facet | Wenhao Li Mengdi Bu Ruiqin Hu Shouwen Jiang Liangbiao Chen George N. Somero |
| author_sort | Wenhao Li |
| collection | DOAJ |
| description | Abstract Background RNA editing by adenosine deaminase acting on RNA (ADAR) occurs in all metazoans and fulfils several functions. Here, we examined effects of acclimation temperature (27 °C, 18 °C,13 °C) on editing patterns in six tissues of zebrafish (Danio rerio). Results Sites and total amounts of editing differed among tissues. Brain showed the highest levels, followed by gill and skin. In these highly edited tissues, decreases in temperatures led to large increases in total amounts of editing and changes in specific edited sites. Gene ontology analysis showed both similarities (e.g., endoplasmic reticulum stress response) and differences in editing among tissues. The majority of edited sites were in transcripts of transposable elements and the 3′UTR regions of protein coding genes. By experimental validation, translation efficiency was directly related to extent of editing of the 3′UTR region of an mRNA. Conclusions RNA editing increases 3′UTR polymorphism and affects efficiency of translation. Such editing may lead to temperature-adaptive changes in the proteome through altering relative amounts of synthesis of different proteins. |
| first_indexed | 2024-03-09T14:55:36Z |
| format | Article |
| id | doaj.art-cd156ed7576b4112b5383934ea59f91d |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-03-09T14:55:36Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj.art-cd156ed7576b4112b5383934ea59f91d2023-11-26T14:14:33ZengBMCBMC Biology1741-70072023-11-0121111610.1186/s12915-023-01738-4Tissue-specific temperature dependence of RNA editing levels in zebrafishWenhao Li0Mengdi Bu1Ruiqin Hu2Shouwen Jiang3Liangbiao Chen4George N. Somero5Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean UniversityKey Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean UniversityKey Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean UniversityKey Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean UniversityKey Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean UniversityDepartment of Biology, Hopkins Marine Station, Stanford UniversityAbstract Background RNA editing by adenosine deaminase acting on RNA (ADAR) occurs in all metazoans and fulfils several functions. Here, we examined effects of acclimation temperature (27 °C, 18 °C,13 °C) on editing patterns in six tissues of zebrafish (Danio rerio). Results Sites and total amounts of editing differed among tissues. Brain showed the highest levels, followed by gill and skin. In these highly edited tissues, decreases in temperatures led to large increases in total amounts of editing and changes in specific edited sites. Gene ontology analysis showed both similarities (e.g., endoplasmic reticulum stress response) and differences in editing among tissues. The majority of edited sites were in transcripts of transposable elements and the 3′UTR regions of protein coding genes. By experimental validation, translation efficiency was directly related to extent of editing of the 3′UTR region of an mRNA. Conclusions RNA editing increases 3′UTR polymorphism and affects efficiency of translation. Such editing may lead to temperature-adaptive changes in the proteome through altering relative amounts of synthesis of different proteins.https://doi.org/10.1186/s12915-023-01738-4AcclimationAdenosine deaminase acting on RNA (ADAR)Corresponding statesRNARNA editingTemperature |
| spellingShingle | Wenhao Li Mengdi Bu Ruiqin Hu Shouwen Jiang Liangbiao Chen George N. Somero Tissue-specific temperature dependence of RNA editing levels in zebrafish BMC Biology Acclimation Adenosine deaminase acting on RNA (ADAR) Corresponding states RNA RNA editing Temperature |
| title | Tissue-specific temperature dependence of RNA editing levels in zebrafish |
| title_full | Tissue-specific temperature dependence of RNA editing levels in zebrafish |
| title_fullStr | Tissue-specific temperature dependence of RNA editing levels in zebrafish |
| title_full_unstemmed | Tissue-specific temperature dependence of RNA editing levels in zebrafish |
| title_short | Tissue-specific temperature dependence of RNA editing levels in zebrafish |
| title_sort | tissue specific temperature dependence of rna editing levels in zebrafish |
| topic | Acclimation Adenosine deaminase acting on RNA (ADAR) Corresponding states RNA RNA editing Temperature |
| url | https://doi.org/10.1186/s12915-023-01738-4 |
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