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Identification and Characterization of 63 MicroRNAs in the Asian Seabass Lates calcarifer

BACKGROUND: MicroRNAs (miRNAs) play an important role in the regulation of many fundamental biological processes. So far miRNAs have been only identified in a few fish species, although there are over 30,000 fish species living under different environmental conditions on the earth. Here, we describe...

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Detalles Bibliográficos
Autores principales: Xia, Jun Hong, He, Xiao Ping, Bai, Zhi Yi, Yue, Gen Hua
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055879/
https://www.ncbi.nlm.nih.gov/pubmed/21412421
http://dx.doi.org/10.1371/journal.pone.0017537
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author Xia, Jun Hong
He, Xiao Ping
Bai, Zhi Yi
Yue, Gen Hua
author_facet Xia, Jun Hong
He, Xiao Ping
Bai, Zhi Yi
Yue, Gen Hua
author_sort Xia, Jun Hong
collection PubMed
description BACKGROUND: MicroRNAs (miRNAs) play an important role in the regulation of many fundamental biological processes. So far miRNAs have been only identified in a few fish species, although there are over 30,000 fish species living under different environmental conditions on the earth. Here, we described an approach to identify conserved miRNAs and characterized their expression patterns in different tissues for the first time in a food fish species Asian seabass (Lates calcarifer). METHODOLOGY/PRINCIPAL FINDINGS: By combining a bioinformatics analysis with an approach of homolog-based PCR amplification and sequencing, 63 novel miRNAs belonging to 29 conserved miRNA families were identified. Of which, 59 miRNAs were conserved across 10–86 species (E value≤10(−4)) and 4 miRNAs were conserved only in fish species. qRT-PCR analysis showed that miR-29, miR-103, miR-125 and several let-7 family members were strongly and ubiquitously expressed in all tissues tested. Interestingly, miR-1, miR-21, miR-183, miR-184 and miR-192 showed highly conserved tissue-specific expression patterns. Exposure of the Asian seabass to lipopolysaccharide (LPS) resulted in up-regulation of over 50% of the identified miRNAs in spleen suggesting the importance of the miRNAs in acute inflammatory immune responses. CONCLUSIONS/SIGNIFICANCE: The approach used in this study is highly effective for identification of conserved miRNAs. The identification of 63 miRNAs and determination of the spatial expression patterns of these miRNAs are valuable resources for further studies on post-transcriptional gene regulation in Asian seabass and other fish species. Further identification of the target genes of these miRNAs would shed new light on their regulatory roles of microRNAs in fish.
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spelling pubmed-30558792011-03-16 Identification and Characterization of 63 MicroRNAs in the Asian Seabass Lates calcarifer Xia, Jun Hong He, Xiao Ping Bai, Zhi Yi Yue, Gen Hua PLoS One Research Article BACKGROUND: MicroRNAs (miRNAs) play an important role in the regulation of many fundamental biological processes. So far miRNAs have been only identified in a few fish species, although there are over 30,000 fish species living under different environmental conditions on the earth. Here, we described an approach to identify conserved miRNAs and characterized their expression patterns in different tissues for the first time in a food fish species Asian seabass (Lates calcarifer). METHODOLOGY/PRINCIPAL FINDINGS: By combining a bioinformatics analysis with an approach of homolog-based PCR amplification and sequencing, 63 novel miRNAs belonging to 29 conserved miRNA families were identified. Of which, 59 miRNAs were conserved across 10–86 species (E value≤10(−4)) and 4 miRNAs were conserved only in fish species. qRT-PCR analysis showed that miR-29, miR-103, miR-125 and several let-7 family members were strongly and ubiquitously expressed in all tissues tested. Interestingly, miR-1, miR-21, miR-183, miR-184 and miR-192 showed highly conserved tissue-specific expression patterns. Exposure of the Asian seabass to lipopolysaccharide (LPS) resulted in up-regulation of over 50% of the identified miRNAs in spleen suggesting the importance of the miRNAs in acute inflammatory immune responses. CONCLUSIONS/SIGNIFICANCE: The approach used in this study is highly effective for identification of conserved miRNAs. The identification of 63 miRNAs and determination of the spatial expression patterns of these miRNAs are valuable resources for further studies on post-transcriptional gene regulation in Asian seabass and other fish species. Further identification of the target genes of these miRNAs would shed new light on their regulatory roles of microRNAs in fish. Public Library of Science 2011-03-11 /pmc/articles/PMC3055879/ /pubmed/21412421 http://dx.doi.org/10.1371/journal.pone.0017537 Text en Xia et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Xia, Jun Hong
He, Xiao Ping
Bai, Zhi Yi
Yue, Gen Hua
Identification and Characterization of 63 MicroRNAs in the Asian Seabass Lates calcarifer
title Identification and Characterization of 63 MicroRNAs in the Asian Seabass Lates calcarifer
title_full Identification and Characterization of 63 MicroRNAs in the Asian Seabass Lates calcarifer
title_fullStr Identification and Characterization of 63 MicroRNAs in the Asian Seabass Lates calcarifer
title_full_unstemmed Identification and Characterization of 63 MicroRNAs in the Asian Seabass Lates calcarifer
title_short Identification and Characterization of 63 MicroRNAs in the Asian Seabass Lates calcarifer
title_sort identification and characterization of 63 micrornas in the asian seabass lates calcarifer
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055879/
https://www.ncbi.nlm.nih.gov/pubmed/21412421
http://dx.doi.org/10.1371/journal.pone.0017537
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