title: Systematic identification and characterization of chicken (Gallus gallus) ncRNAs.
abstract: 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.
authors.affiliation: National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.forename: Shoujun
authors.initials: S
authors.lastname: Huang
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.forename: Ning
authors.initials: N
authors.lastname: Yang
authors.forename: Dandan
authors.initials: D
authors.lastname: Song
authors.forename: Rimao
authors.initials: R
authors.lastname: Wu
authors.forename: Wei
authors.initials: W
authors.lastname: Deng
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerbø
authors.forename: Xiu-Jie
authors.initials: XJ
authors.lastname: Wang
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
authors.forename: Dahai
authors.initials: D
authors.lastname: Zhu
mesh_terms: 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*
chemical_list: D020537:RNA, Small Nucleolar; D022661:RNA, Untranslated