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Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data

Current technologies that are used for genome-wide microRNA (miRNA) prediction are mainly based on BLAST tool. They often produce a large number of false positives. Here, we describe an effective approach for identifying orthologous pre-miRNAs in several primates based on syntenic information. Some...

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Autores principales: Yuan, Zhidong, Liu, Hongde, Nie, Yumin, Ding, Suping, Yan, Mingli, Tan, Shuhua, Jin, Yuanchang, Sun, Xiao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Molecular Diversity Preservation International (MDPI) 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3821645/
https://www.ncbi.nlm.nih.gov/pubmed/24135875
http://dx.doi.org/10.3390/ijms141020820
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author Yuan, Zhidong
Liu, Hongde
Nie, Yumin
Ding, Suping
Yan, Mingli
Tan, Shuhua
Jin, Yuanchang
Sun, Xiao
author_facet Yuan, Zhidong
Liu, Hongde
Nie, Yumin
Ding, Suping
Yan, Mingli
Tan, Shuhua
Jin, Yuanchang
Sun, Xiao
author_sort Yuan, Zhidong
collection PubMed
description Current technologies that are used for genome-wide microRNA (miRNA) prediction are mainly based on BLAST tool. They often produce a large number of false positives. Here, we describe an effective approach for identifying orthologous pre-miRNAs in several primates based on syntenic information. Some of them have been validated by small RNA high throughput sequencing data. This approach uses the synteny information and experimentally validated miRNAs of human, and incorporates currently available algorithms and tools to identify the pre-miRNAs in five other primates. First, we identified 929 potential pre-miRNAs in the marmoset in which miRNAs have not yet been reported. Then, we predicted the miRNAs in other primates, and we successfully re-identified most of the published miRNAs and found 721, 979, 650 and 639 new potential pre-miRNAs in chimpanzee, gorilla, orangutan and rhesus macaque, respectively. Furthermore, the miRNA transcriptome in the four primates have been re-analyzed and some novel predicted miRNAs have been supported by the small RNA sequencing data. Finally, we analyzed the potential functions of those validated miRNAs and explored the regulatory elements and transcription factors of some validated miRNA genes of interest. The results show that our approach can effectively identify novel miRNAs and some miRNAs that supported by small RNA sequencing data maybe play roles in the nervous system.
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spelling pubmed-38216452013-11-11 Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data Yuan, Zhidong Liu, Hongde Nie, Yumin Ding, Suping Yan, Mingli Tan, Shuhua Jin, Yuanchang Sun, Xiao Int J Mol Sci Article Current technologies that are used for genome-wide microRNA (miRNA) prediction are mainly based on BLAST tool. They often produce a large number of false positives. Here, we describe an effective approach for identifying orthologous pre-miRNAs in several primates based on syntenic information. Some of them have been validated by small RNA high throughput sequencing data. This approach uses the synteny information and experimentally validated miRNAs of human, and incorporates currently available algorithms and tools to identify the pre-miRNAs in five other primates. First, we identified 929 potential pre-miRNAs in the marmoset in which miRNAs have not yet been reported. Then, we predicted the miRNAs in other primates, and we successfully re-identified most of the published miRNAs and found 721, 979, 650 and 639 new potential pre-miRNAs in chimpanzee, gorilla, orangutan and rhesus macaque, respectively. Furthermore, the miRNA transcriptome in the four primates have been re-analyzed and some novel predicted miRNAs have been supported by the small RNA sequencing data. Finally, we analyzed the potential functions of those validated miRNAs and explored the regulatory elements and transcription factors of some validated miRNA genes of interest. The results show that our approach can effectively identify novel miRNAs and some miRNAs that supported by small RNA sequencing data maybe play roles in the nervous system. Molecular Diversity Preservation International (MDPI) 2013-10-16 /pmc/articles/PMC3821645/ /pubmed/24135875 http://dx.doi.org/10.3390/ijms141020820 Text en © 2013 by the authors; licensee MDPI, Basel, Switzerland http://creativecommons.org/licenses/by/3.0/ This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Article
Yuan, Zhidong
Liu, Hongde
Nie, Yumin
Ding, Suping
Yan, Mingli
Tan, Shuhua
Jin, Yuanchang
Sun, Xiao
Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data
title Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data
title_full Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data
title_fullStr Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data
title_full_unstemmed Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data
title_short Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data
title_sort identification of novel micrornas in primates by using the synteny information and small rna deep sequencing data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3821645/
https://www.ncbi.nlm.nih.gov/pubmed/24135875
http://dx.doi.org/10.3390/ijms141020820
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