Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals.
Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals.
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DOI：
10.1101/gr.165035.113
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发表时间：
2014-04
期刊：
影响因子：
7
通讯作者：
Garber M
中科院分区：
文献类型：
--
作者：
Washietl S;Kellis M;Garber M
长基因间非编码RNA（lincRNA）在人类发育和疾病中发挥着多种调控作用，但对其进化历史和限制因素知之甚少。在这里，我们描述了人类lincRNA的表达模式在九个组织在六个哺乳动物物种和多个人。在这些组织中表达的1898种人类lincRNA中，我们发现黑猩猩中有80%的正向转录本，恒河猴中有63%，牛中有39%，小鼠中有38%，大鼠中有35%。哺乳动物表达的lincRNA显示出非常强的组织特异性保守性，表明它是选择性维持的。相反，丰富的剪接位点营业额表明，确切的剪接位点并不重要。相对于进化上年轻的lincRNA，在其启动子和外显子中，拟南芥表达的lincRNA显示出更高的一级序列保守性，增加了与富含组织特异性功能的蛋白质编码基因的接近性，更少的重复元件，以及更频繁的单外显子转录本。值得注意的是，我们发现超过20%的人类lincRNA在黑猩猩之外没有表达，甚至在恒河猴中也检测不到。这些原始人特异性lincRNA更具组织特异性，富含睾丸，并且在人类谱系内进化更快。
Long intergenic noncoding RNAs (lincRNAs) play diverse regulatory roles in human development and disease, but little is known about their evolutionary history and constraint. Here, we characterize human lincRNA expression patterns in nine tissues across six mammalian species and multiple individuals. Of the 1898 human lincRNAs expressed in these tissues, we find orthologous transcripts for 80% in chimpanzee, 63% in rhesus, 39% in cow, 38% in mouse, and 35% in rat. Mammalian-expressed lincRNAs show remarkably strong conservation of tissue specificity, suggesting that it is selectively maintained. In contrast, abundant splice-site turnover suggests that exact splice sites are not critical. Relative to evolutionarily young lincRNAs, mammalian-expressed lincRNAs show higher primary sequence conservation in their promoters and exons, increased proximity to protein-coding genes enriched for tissue-specific functions, fewer repeat elements, and more frequent single-exon transcripts. Remarkably, we find that ∼20% of human lincRNAs are not expressed beyond chimpanzee and are undetectable even in rhesus. These hominid-specific lincRNAs are more tissue specific, enriched for testis, and faster evolving within the human lineage.
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影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
来自1,092个人基因组的遗传变异的综合图。
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
4.5
作者：
Kutter C;Watt S;Stefflova K;Wilson MD;Goncalves A;Ponting CP;Odom DT;Marques AC
通讯作者：
Marques AC
影响因子：
14.9
作者：
Flicek P;Ahmed I;Amode MR;Barrell D;Beal K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fairley S;Fitzgerald S;Gil L;García-Girón C;Gordon L;Hourlier T;Hunt S;Juettemann T;Kähäri AK;Keenan S;Komorowska M;Kulesha E;Longden I;Maurel T;McLaren WM;Muffato M;Nag R;Overduin B;Pignatelli M;Pritchard B;Pritchard E;Riat HS;Ritchie GR;Ruffier M;Schuster M;Sheppard D;Sobral D;Taylor K;Thormann A;Trevanion S;White S;Wilder SP;Aken BL;Birney E;Cunningham F;Dunham I;Harrow J;Herrero J;Hubbard TJ;Johnson N;Kinsella R;Parker A;Spudich G;Yates A;Zadissa A;Searle SM
通讯作者：
Searle SM
影响因子：
10.5
作者：
Cabili, Moran N.;Trapnell, Cole;Rinn, John L.
通讯作者：
Rinn, John L.