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 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.
Zhang
Yong
Y
National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.
Wang
Jie
J
Huang
Shoujun
S
Zhu
Xiaopeng
X
Liu
Jun
J
Yang
Ning
N
Song
Dandan
D
Wu
Rimao
R
Deng
Wei
W
Skogerbø
Geir
G
Wang
Xiu-Jie
XJ
Chen
Runsheng
R
Zhu
Dahai
D
D000818:Animals; D001483:Base Sequence; D002645:Chickens / Q000235:genetics* / Q000254:growth & development; D007438:Introns; D008969:Molecular Sequence Data; D012326:RNA Splicing; D020537:RNA, Small Nucleolar / Q000378:metabolism; D022661:RNA, Untranslated / Q000032:analysis / Q000145:classification / Q000378:metabolism*
D020537:RNA, Small Nucleolar; D022661:RNA, Untranslated