Systematic identification and characterization of chicken (Gallus gallus) ncRNAs
Systematic identification and characterization of chicken (Gallus gallus) ncRNAs
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鸡 (Gallus gallus) ncRNA 的系统鉴定和表征
DOI：
10.1093/nar/gkp704
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发表时间：
2009-08
影响因子：
14.9
通讯作者：
Yang, Ning
中科院分区：
文献类型：
--
作者：
Wang, Jie;Song, D;an;Wang, Xiu-Jie;Zhu, Dahai;Deng, Wei;Chen, Runsheng;Skogerbo, Geir;Wu, Rimao;Liu, Jun;Zhu, Xiaopeng;Zhang, Yong;Huang, Shoujun;Yang, Ning
近年来的研究表明，非编码RNA（non-coding RNA，ncRNA）在发育和进化过程中发挥着重要作用。鸡是第一个获得基因组测序的非哺乳动物，具有独特的发育和进化研究特征。然而，除了microRNA，关于鸡ncRNA的信息主要是从计算预测中获得的，没有实验验证。在本研究中，我们进行了系统的鉴定中等大小的ncRNA（50-500 nt）的ncRNA文库的构建和鉴定125鸡ncRNA。重要的是，通过生物信息学和表达分析，我们发现鸡的ncRNA具有几个新的特征：（i）与18个已测序的脊椎动物基因组的比较基因组分析显示，大多数新鉴定的ncRNA候选者是不保守的，大多数是潜在的鸟类/鸡特异性的，这表明ncRNA在进化过程中起着谱系/物种规范的作用。(ii)内含子snoRNA与宿主基因的表达模式分析表明snoRNA与宿主基因之间存在协同表达。(iii)一些时空特异性表达模式表明ncRNA参与组织发育。总之，这些发现为未来ncRNA在发育和进化过程中的功能研究提供了新的线索。
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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影响因子：
56.9
作者：
Cheng, J;Kapranov, P;Gingeras, TR
通讯作者：
Gingeras, TR
影响因子：
3.5
作者：
Peng Shao;Hui Zhou;Zhen-Dong Xiao;Jie-hua He;Mian-bo Huang;Yue‐Qin Chen;L. Qu
通讯作者：
Peng Shao;Hui Zhou;Zhen-Dong Xiao;Jie-hua He;Mian-bo Huang;Yue‐Qin Chen;L. Qu
影响因子：
56.9
作者：
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通讯作者：
Snyder, M
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影响因子：
14.9
作者：
Zheng Q;Wang XJ
通讯作者：
Wang XJ
影响因子：
64.5
作者：
Balakin, AG;Smith, L;Fournier, MJ
通讯作者：
Fournier, MJ