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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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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2011
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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. |
format | Text |
id | pubmed-3055879 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
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
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title_full | Identification and Characterization of 63 MicroRNAs in the Asian Seabass Lates calcarifer
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title_fullStr | Identification and Characterization of 63 MicroRNAs in the Asian Seabass Lates calcarifer
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title_full_unstemmed | Identification and Characterization of 63 MicroRNAs in the Asian Seabass Lates calcarifer
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title_short | Identification and Characterization of 63 MicroRNAs in the Asian Seabass Lates calcarifer
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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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