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Systematic identification and characterization of chicken (Gallus gallus) ncRNAs

Recent studies have demonstrated that non-coding RNAs (ncRNAs) play important roles during development and evolution. Chicken, the first genome-sequenced non-mammalian amniote, possesses unique features for developmental and evolutionary studies. However, apart from microRNAs, information on chicken...

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Autores principales: Zhang, Yong, Wang, Jie, Huang, Shoujun, Zhu, Xiaopeng, Liu, Jun, Yang, Ning, Song, Dandan, Wu, Rimao, Deng, Wei, Skogerbø, Geir, Wang, Xiu-Jie, Chen, Runsheng, Zhu, Dahai
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770669/
https://www.ncbi.nlm.nih.gov/pubmed/19720738
http://dx.doi.org/10.1093/nar/gkp704
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author Zhang, Yong
Wang, Jie
Huang, Shoujun
Zhu, Xiaopeng
Liu, Jun
Yang, Ning
Song, Dandan
Wu, Rimao
Deng, Wei
Skogerbø, Geir
Wang, Xiu-Jie
Chen, Runsheng
Zhu, Dahai
author_facet Zhang, Yong
Wang, Jie
Huang, Shoujun
Zhu, Xiaopeng
Liu, Jun
Yang, Ning
Song, Dandan
Wu, Rimao
Deng, Wei
Skogerbø, Geir
Wang, Xiu-Jie
Chen, Runsheng
Zhu, Dahai
author_sort Zhang, Yong
collection PubMed
description Recent studies have demonstrated that non-coding RNAs (ncRNAs) play important roles during development and evolution. Chicken, the first genome-sequenced non-mammalian amniote, possesses unique features for developmental and evolutionary studies. However, apart from microRNAs, information on chicken ncRNAs has mainly been obtained from computational predictions without experimental validation. In the present study, we performed a systematic identification of intermediate size ncRNAs (50–500 nt) by ncRNA library construction and identified 125 chicken ncRNAs. Importantly, through the bioinformatics and expression analysis, we found the chicken ncRNAs has several novel features: (i) comparative genomic analysis against 18 sequenced vertebrate genomes revealed that the majority of the newly identified ncRNA candidates is not conserved and most are potentially bird/chicken specific, suggesting that ncRNAs play roles in lineage/species specification during evolution. (ii) The expression pattern analysis of intronic snoRNAs and their host genes suggested the coordinated expression between snoRNAs and their host genes. (iii) Several spatio-temporal specific expression patterns suggest involvement of ncRNAs in tissue development. Together, these findings provide new clues for future functional study of ncRNAs during development and evolution.
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spelling pubmed-27706692009-10-30 Systematic identification and characterization of chicken (Gallus gallus) ncRNAs Zhang, Yong Wang, Jie Huang, Shoujun Zhu, Xiaopeng Liu, Jun Yang, Ning Song, Dandan Wu, Rimao Deng, Wei Skogerbø, Geir Wang, Xiu-Jie Chen, Runsheng Zhu, Dahai Nucleic Acids Res RNA Recent studies have demonstrated that non-coding RNAs (ncRNAs) play important roles during development and evolution. Chicken, the first genome-sequenced non-mammalian amniote, possesses unique features for developmental and evolutionary studies. However, apart from microRNAs, information on chicken ncRNAs has mainly been obtained from computational predictions without experimental validation. In the present study, we performed a systematic identification of intermediate size ncRNAs (50–500 nt) by ncRNA library construction and identified 125 chicken ncRNAs. Importantly, through the bioinformatics and expression analysis, we found the chicken ncRNAs has several novel features: (i) comparative genomic analysis against 18 sequenced vertebrate genomes revealed that the majority of the newly identified ncRNA candidates is not conserved and most are potentially bird/chicken specific, suggesting that ncRNAs play roles in lineage/species specification during evolution. (ii) The expression pattern analysis of intronic snoRNAs and their host genes suggested the coordinated expression between snoRNAs and their host genes. (iii) Several spatio-temporal specific expression patterns suggest involvement of ncRNAs in tissue development. Together, these findings provide new clues for future functional study of ncRNAs during development and evolution. Oxford University Press 2009-10 2009-08-31 /pmc/articles/PMC2770669/ /pubmed/19720738 http://dx.doi.org/10.1093/nar/gkp704 Text en © The Author(s) 2009. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle RNA
Zhang, Yong
Wang, Jie
Huang, Shoujun
Zhu, Xiaopeng
Liu, Jun
Yang, Ning
Song, Dandan
Wu, Rimao
Deng, Wei
Skogerbø, Geir
Wang, Xiu-Jie
Chen, Runsheng
Zhu, Dahai
Systematic identification and characterization of chicken (Gallus gallus) ncRNAs
title Systematic identification and characterization of chicken (Gallus gallus) ncRNAs
title_full Systematic identification and characterization of chicken (Gallus gallus) ncRNAs
title_fullStr Systematic identification and characterization of chicken (Gallus gallus) ncRNAs
title_full_unstemmed Systematic identification and characterization of chicken (Gallus gallus) ncRNAs
title_short Systematic identification and characterization of chicken (Gallus gallus) ncRNAs
title_sort systematic identification and characterization of chicken (gallus gallus) ncrnas
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770669/
https://www.ncbi.nlm.nih.gov/pubmed/19720738
http://dx.doi.org/10.1093/nar/gkp704
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