Nucleic Acids Research Advance Access originally published online on August 31, 2009
Nucleic Acids Research 2009 37(19):6562-6574; doi:10.1093/nar/gkp704
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Nucleic Acids Research, 2009, Vol. 37, No. 19 6562-6574
© The Author(s) 2009. Published by Oxford University Press.
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.
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Systematic identification and characterization of chicken (Gallus gallus) ncRNAs
1National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, 2Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, 3State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Beijing 100101, 4Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100094 and 5Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
*To whom correspondence should be addressed. Tel: +86 10 65296949; Fax: +86 10 65105083; Email: dhzhu{at}pumc.edu.cn
Correspondence may also be addressed to Runsheng Chen. Tel: +86 10 64888543; Fax: +86 10 64889892; Email: crs{at}sun5.ibp.ac.cn
Received December 2, 2008. Revised July 25, 2009. Accepted August 10, 2009.
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.
The authors wish it to be known that, in their opinion, the first four authors should be regarded as joint First Authors.