Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data.
Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data.
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从现有转录组数据中鉴定和表征与小鼠胚胎脑发育相关的长非编码 RNA
DOI：
10.1371/journal.pone.0071152
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Wu Q
中科院分区：
文献类型：
--
作者：
Lv J;Cui W;Liu H;He H;Xiu Y;Guo J;Liu H;Liu Q;Zeng T;Chen Y;Zhang Y;Wu Q
长链非编码RNA（lncRNA）作为一类重要的非编码RNA，受到了广泛的关注。虽然lncRNA在高等哺乳动物中已被系统地研究和功能注释，但很少有系统的鉴定和注释。由于lncRNA表达的特异性，已知的在胚胎脑组织中表达的lncRNA仍然有限。考虑到大量lncRNA仅在脑组织中转录，因此对发育脑中lncRNA的研究具有特殊意义。在这里，胚胎脑中公开可用的RNA测序（RNA-seq）数据被整合，以通过定制的管道识别数千种胚胎脑lncRNA。一个新的转录本的显着比例还没有注释的可用基因组资源。假定的胚胎脑lncRNA长度较短，剪接较少，并且比已知基因显示出较少的保守性。推测的lncRNA的表达量平均为已知编码基因的十分之一，而与已知的lncRNA相当。根据染色质数据，推定的胚胎脑lncRNA与活性染色质标记相关，与已知的lncRNA相当。胚胎脑表达的lncRNA也表明具有表达，尽管在成人脑中不明显。对推定的胚胎脑lncRNA的基因本体论分析表明它们与脑发育相关。推测的lncRNA被证明与可能的顺式调节作用有关，即使它们本身被认为是印迹lncRNA。对一个敲除数据的重新分析表明，四个调节子与lncRNA相关。两者合计，推定lncRNA的鉴定和系统分析将提供新的见解，未表征的小鼠非编码区和与哺乳动物胚胎脑发育的关系。
Long non-coding RNAs (lncRNAs) as a key group of non-coding RNAs have gained widely attention. Though lncRNAs have been functionally annotated and systematic explored in higher mammals, few are under systematical identification and annotation. Owing to the expression specificity, known lncRNAs expressed in embryonic brain tissues remain still limited. Considering a large number of lncRNAs are only transcribed in brain tissues, studies of lncRNAs in developmental brain are therefore of special interest. Here, publicly available RNA-sequencing (RNA-seq) data in embryonic brain are integrated to identify thousands of embryonic brain lncRNAs by a customized pipeline. A significant proportion of novel transcripts have not been annotated by available genomic resources. The putative embryonic brain lncRNAs are shorter in length, less spliced and show less conservation than known genes. The expression of putative lncRNAs is in one tenth on average of known coding genes, while comparable with known lncRNAs. From chromatin data, putative embryonic brain lncRNAs are associated with active chromatin marks, comparable with known lncRNAs. Embryonic brain expressed lncRNAs are also indicated to have expression though not evident in adult brain. Gene Ontology analysis of putative embryonic brain lncRNAs suggests that they are associated with brain development. The putative lncRNAs are shown to be related to possible cis-regulatory roles in imprinting even themselves are deemed to be imprinted lncRNAs. Re-analysis of one knockdown data suggests that four regulators are associated with lncRNAs. Taken together, the identification and systematic analysis of putative lncRNAs would provide novel insights into uncharacterized mouse non-coding regions and the relationships with mammalian embryonic brain development.
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影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
通过RNA-Seq对印迹基因表达的批判性评估：一种新的观点。
影响因子：
4.5
作者：
DeVeale B;van der Kooy D;Babak T
通讯作者：
Babak T
影响因子：
14.9
作者：
Dimmer EC;Huntley RP;Alam-Faruque Y;Sawford T;O'Donovan C;Martin MJ;Bely B;Browne P;Mun Chan W;Eberhardt R;Gardner M;Laiho K;Legge D;Magrane M;Pichler K;Poggioli D;Sehra H;Auchincloss A;Axelsen K;Blatter MC;Boutet E;Braconi-Quintaje S;Breuza L;Bridge A;Coudert E;Estreicher A;Famiglietti L;Ferro-Rojas S;Feuermann M;Gos A;Gruaz-Gumowski N;Hinz U;Hulo C;James J;Jimenez S;Jungo F;Keller G;Lemercier P;Lieberherr D;Masson P;Moinat M;Pedruzzi I;Poux S;Rivoire C;Roechert B;Schneider M;Stutz A;Sundaram S;Tognolli M;Bougueleret L;Argoud-Puy G;Cusin I;Duek-Roggli P;Xenarios I;Apweiler R
通讯作者：
Apweiler R
影响因子：
14.9
作者：
Dreszer TR;Karolchik D;Zweig AS;Hinrichs AS;Raney BJ;Kuhn RM;Meyer LR;Wong M;Sloan CA;Rosenbloom KR;Roe G;Rhead B;Pohl A;Malladi VS;Li CH;Learned K;Kirkup V;Hsu F;Harte RA;Guruvadoo L;Goldman M;Giardine BM;Fujita PA;Diekhans M;Cline MS;Clawson H;Barber GP;Haussler D;James Kent W
通讯作者：
James Kent W
影响因子：
3.5
作者：
Alfano, G;Vitiello, C;Banfi, S
通讯作者：
Banfi, S