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- Scopus: eid_2-s2.0-85185474370
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Article: Long non-coding RNAs mediate fish gene expression in response to ocean acidification
Title | Long non-coding RNAs mediate fish gene expression in response to ocean acidification |
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Authors | |
Keywords | annotation environmental change epigenetic regulation lncRNAs ocean acidification RNA sequencing |
Issue Date | 14-Feb-2024 |
Publisher | Wiley Open Access |
Citation | Evolutionary Applications, 2024, v. 17, n. 2 How to Cite? |
Abstract | The majority of the transcribed genome does not have coding potential but these non-coding transcripts play crucial roles in transcriptional and post-transcriptional regulation of protein-coding genes. Regulation of gene expression is important in shaping an organism's response to environmental changes, ultimately impacting their survival and persistence as population or species face global change. However, the roles of long non-coding RNAs (lncRNAs), when confronted with environmental changes, remain largely unclear. To explore the potential role of lncRNAs in fish exposed to ocean acidification (OA), we analyzed publicly available brain RNA-seq data from a coral reef fish Acanthochromis polyacanthus. We annotated the lncRNAs in its genome and examined the expression changes of intergenic lncRNAs (lincRNAs) between A. polyacanthus samples from a natural CO2 seep and a nearby control site. We identified 4728 lncRNAs, including 3272 lincRNAs in this species. Remarkably, 93.03% of these lincRNAs were species-specific. Among the 125 highly expressed lincRNAs and 403 differentially expressed lincRNAs in response to elevated CO2, we observed that lincRNAs were either neighboring or potentially trans-regulating differentially expressed coding genes associated with pH regulation, neural signal transduction, and ion transport, which are known to be important in the response to OA in fish. In summary, lncRNAs may facilitate fish acclimation and mediate the responses of fish to OA by modulating the expression of crucial coding genes, which offers insight into the regulatory mechanisms underlying fish responses to environmental changes. |
Persistent Identifier | http://hdl.handle.net/10722/344693 |
ISSN | 2020 SCImago Journal Rankings: 1.776 |
DC Field | Value | Language |
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dc.contributor.author | Kang, Jingliang | - |
dc.contributor.author | Chung, Arthur | - |
dc.contributor.author | Suresh, Sneha | - |
dc.contributor.author | Bonzi, Lucrezia C. | - |
dc.contributor.author | Sourisse, Jade M. | - |
dc.contributor.author | Ramirez-Calero, Sandra | - |
dc.contributor.author | Romeo, Daniele | - |
dc.contributor.author | Petit-Marty, Natalia | - |
dc.contributor.author | Pegueroles, Cinta | - |
dc.contributor.author | Schunter, Celia | - |
dc.date.accessioned | 2024-08-02T04:43:45Z | - |
dc.date.available | 2024-08-02T04:43:45Z | - |
dc.date.issued | 2024-02-14 | - |
dc.identifier.citation | Evolutionary Applications, 2024, v. 17, n. 2 | - |
dc.identifier.issn | 1752-4563 | - |
dc.identifier.uri | http://hdl.handle.net/10722/344693 | - |
dc.description.abstract | The majority of the transcribed genome does not have coding potential but these non-coding transcripts play crucial roles in transcriptional and post-transcriptional regulation of protein-coding genes. Regulation of gene expression is important in shaping an organism's response to environmental changes, ultimately impacting their survival and persistence as population or species face global change. However, the roles of long non-coding RNAs (lncRNAs), when confronted with environmental changes, remain largely unclear. To explore the potential role of lncRNAs in fish exposed to ocean acidification (OA), we analyzed publicly available brain RNA-seq data from a coral reef fish Acanthochromis polyacanthus. We annotated the lncRNAs in its genome and examined the expression changes of intergenic lncRNAs (lincRNAs) between A. polyacanthus samples from a natural CO2 seep and a nearby control site. We identified 4728 lncRNAs, including 3272 lincRNAs in this species. Remarkably, 93.03% of these lincRNAs were species-specific. Among the 125 highly expressed lincRNAs and 403 differentially expressed lincRNAs in response to elevated CO2, we observed that lincRNAs were either neighboring or potentially trans-regulating differentially expressed coding genes associated with pH regulation, neural signal transduction, and ion transport, which are known to be important in the response to OA in fish. In summary, lncRNAs may facilitate fish acclimation and mediate the responses of fish to OA by modulating the expression of crucial coding genes, which offers insight into the regulatory mechanisms underlying fish responses to environmental changes. | - |
dc.language | eng | - |
dc.publisher | Wiley Open Access | - |
dc.relation.ispartof | Evolutionary Applications | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | annotation | - |
dc.subject | environmental change | - |
dc.subject | epigenetic regulation | - |
dc.subject | lncRNAs | - |
dc.subject | ocean acidification | - |
dc.subject | RNA sequencing | - |
dc.title | Long non-coding RNAs mediate fish gene expression in response to ocean acidification | - |
dc.type | Article | - |
dc.identifier.doi | 10.1111/eva.13655 | - |
dc.identifier.scopus | eid_2-s2.0-85185474370 | - |
dc.identifier.volume | 17 | - |
dc.identifier.issue | 2 | - |
dc.identifier.eissn | 1752-4571 | - |
dc.identifier.issnl | 1752-4571 | - |