Cargando…

Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs

BACKGROUND: Recent studies have demonstrated that non-protein-coding RNAs (npcRNAs/ncRNAs) play important roles during eukaryotic development, species evolution, and in the etiology of disease. Rhesus macaques are the most widely used primate model in both biomedical research and primate evolutionar...

Descripción completa

Detalles Bibliográficos
Autores principales: Zhang, Yong, Liu, Jun, Jia, Chunshi, Li, Tingting, Wu, Rimao, Wang, Jie, Chen, Ying, Zou, Xiaoting, Chen, Runsheng, Wang, Xiu-Jie, Zhu, Dahai
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832892/
https://www.ncbi.nlm.nih.gov/pubmed/20100322
http://dx.doi.org/10.1186/1471-2164-11-61
_version_ 1782178352249962496
author Zhang, Yong
Liu, Jun
Jia, Chunshi
Li, Tingting
Wu, Rimao
Wang, Jie
Chen, Ying
Zou, Xiaoting
Chen, Runsheng
Wang, Xiu-Jie
Zhu, Dahai
author_facet Zhang, Yong
Liu, Jun
Jia, Chunshi
Li, Tingting
Wu, Rimao
Wang, Jie
Chen, Ying
Zou, Xiaoting
Chen, Runsheng
Wang, Xiu-Jie
Zhu, Dahai
author_sort Zhang, Yong
collection PubMed
description BACKGROUND: Recent studies have demonstrated that non-protein-coding RNAs (npcRNAs/ncRNAs) play important roles during eukaryotic development, species evolution, and in the etiology of disease. Rhesus macaques are the most widely used primate model in both biomedical research and primate evolutionary studies. However, most reports on these animals focus on the functional roles of protein-coding sequences, whereas very little is known about macaque ncRNAs. RESULTS: In the present study, we performed the first systematic profiling of intermediate-size ncRNAs (50 to 500 nt) from the rhesus monkey by constructing a cDNA library. We identified 117 rhesus monkey ncRNAs, including 80 small nucleolar RNAs (snoRNAs), 29 other types of known RNAs (snRNAs, Y RNA, and others), and eight unclassified ncRNAs. Comparative genomic analysis and northern blot hybridizations demonstrated that some snoRNAs were lineage- or species-specific. Paralogous sequences were found for most rhesus monkey snoRNAs, the expression of which might be attributable to extensive duplication within the rhesus monkey genome. Further investigation of snoRNA flanking sequences showed that some rhesus monkey snoRNAs are retrogenes derived from L1-mediated integration. Finally, phylogenetic analysis demonstrated that birds and primates share some snoRNAs and host genes thereof, suggesting that both the relevant host genes and the snoRNAs contained therein may be inherited from a common ancestor. However, some rhesus monkey snoRNAs hosted by non-ribosome-related genes appeared after the evolutionary divergence between birds and mammals. CONCLUSIONS: We provide the first experimentally-derived catalog of rhesus monkey ncRNAs and uncover some interesting genomic and evolutionary features. These findings provide important information for future functional characterization of snoRNAs during primate evolution.
format Text
id pubmed-2832892
institution National Center for Biotechnology Information
language English
publishDate 2010
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-28328922010-03-06 Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs Zhang, Yong Liu, Jun Jia, Chunshi Li, Tingting Wu, Rimao Wang, Jie Chen, Ying Zou, Xiaoting Chen, Runsheng Wang, Xiu-Jie Zhu, Dahai BMC Genomics Research Article BACKGROUND: Recent studies have demonstrated that non-protein-coding RNAs (npcRNAs/ncRNAs) play important roles during eukaryotic development, species evolution, and in the etiology of disease. Rhesus macaques are the most widely used primate model in both biomedical research and primate evolutionary studies. However, most reports on these animals focus on the functional roles of protein-coding sequences, whereas very little is known about macaque ncRNAs. RESULTS: In the present study, we performed the first systematic profiling of intermediate-size ncRNAs (50 to 500 nt) from the rhesus monkey by constructing a cDNA library. We identified 117 rhesus monkey ncRNAs, including 80 small nucleolar RNAs (snoRNAs), 29 other types of known RNAs (snRNAs, Y RNA, and others), and eight unclassified ncRNAs. Comparative genomic analysis and northern blot hybridizations demonstrated that some snoRNAs were lineage- or species-specific. Paralogous sequences were found for most rhesus monkey snoRNAs, the expression of which might be attributable to extensive duplication within the rhesus monkey genome. Further investigation of snoRNA flanking sequences showed that some rhesus monkey snoRNAs are retrogenes derived from L1-mediated integration. Finally, phylogenetic analysis demonstrated that birds and primates share some snoRNAs and host genes thereof, suggesting that both the relevant host genes and the snoRNAs contained therein may be inherited from a common ancestor. However, some rhesus monkey snoRNAs hosted by non-ribosome-related genes appeared after the evolutionary divergence between birds and mammals. CONCLUSIONS: We provide the first experimentally-derived catalog of rhesus monkey ncRNAs and uncover some interesting genomic and evolutionary features. These findings provide important information for future functional characterization of snoRNAs during primate evolution. BioMed Central 2010-01-25 /pmc/articles/PMC2832892/ /pubmed/20100322 http://dx.doi.org/10.1186/1471-2164-11-61 Text en Copyright ©2010 Zhang et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Zhang, Yong
Liu, Jun
Jia, Chunshi
Li, Tingting
Wu, Rimao
Wang, Jie
Chen, Ying
Zou, Xiaoting
Chen, Runsheng
Wang, Xiu-Jie
Zhu, Dahai
Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs
title Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs
title_full Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs
title_fullStr Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs
title_full_unstemmed Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs
title_short Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs
title_sort systematic identification and evolutionary features of rhesus monkey small nucleolar rnas
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832892/
https://www.ncbi.nlm.nih.gov/pubmed/20100322
http://dx.doi.org/10.1186/1471-2164-11-61
work_keys_str_mv AT zhangyong systematicidentificationandevolutionaryfeaturesofrhesusmonkeysmallnucleolarrnas
AT liujun systematicidentificationandevolutionaryfeaturesofrhesusmonkeysmallnucleolarrnas
AT jiachunshi systematicidentificationandevolutionaryfeaturesofrhesusmonkeysmallnucleolarrnas
AT litingting systematicidentificationandevolutionaryfeaturesofrhesusmonkeysmallnucleolarrnas
AT wurimao systematicidentificationandevolutionaryfeaturesofrhesusmonkeysmallnucleolarrnas
AT wangjie systematicidentificationandevolutionaryfeaturesofrhesusmonkeysmallnucleolarrnas
AT chenying systematicidentificationandevolutionaryfeaturesofrhesusmonkeysmallnucleolarrnas
AT zouxiaoting systematicidentificationandevolutionaryfeaturesofrhesusmonkeysmallnucleolarrnas
AT chenrunsheng systematicidentificationandevolutionaryfeaturesofrhesusmonkeysmallnucleolarrnas
AT wangxiujie systematicidentificationandevolutionaryfeaturesofrhesusmonkeysmallnucleolarrnas
AT zhudahai systematicidentificationandevolutionaryfeaturesofrhesusmonkeysmallnucleolarrnas