Human microRNAs originated from two periods at accelerated rates in mammalian evolution.
Human microRNAs originated from two periods at accelerated rates in mammalian evolution.
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DOI：
10.1093/molbev/mss262
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发表时间：
2013-03
影响因子：
10.7
通讯作者：
Masaki T
中科院分区：
文献类型：
--
作者：
Iwama H;Kato K;Imachi H;Murao K;Masaki T
MicroRNA (miRNA) 是短的非编码 RNA，可在转录后调节基因。据报道，在进化过程中会频繁发生 miRNA 基因的获得和丢失。然而，人们对现存哺乳动物物种现有 miRNA 基因库的进化起源时期知之甚少。因此，在这项研究中，我们主要使用 38 个物种的多重基因组比对，加上 5 个物种的成对基因组比对，估计了 1,433 个现有人类 miRNA 基因中每一个起源于 15 个时期内的进化时期，从人类到鸭嘴兽——人类共同祖先分支和“兽亚纲之外保守的”类别。结果显示，人类 miRNA 基因起源的速度显着加快有两个高峰期。最快的速率出现在类人猿谱系的初始阶段，第二个速率出现在劳亚兽分化之前不久。目前大约 53% 的人类 miRNA 基因起源于人类的猿猴谱系。特别是，大约 28% 起源于类人猿谱系。胎盘哺乳动物辐射的早期阶段约占 28%，而在胎盘哺乳动物之外，不超过 15% 的人类 miRNA 是保守的。我们还清楚地显示了一个总体趋势，即 miRNA 表达水平随着 miRNA 变年轻而降低。有趣的是，在这种表达下降的趋势中，我们发现与类人猿谱系的初始阶段相对应的表达水平显着上升，这表明 miRNA 功能获取的增加起源于这一特定时期。
MicroRNAs (miRNAs) are short, noncoding RNAs that modulate genes posttranscriptionally. Frequent gains and losses of miRNA genes have been reported to occur during evolution. However, little is known systematically about the periods of evolutionary origin of the present miRNA gene repertoire of an extant mammalian species. Thus, in this study, we estimated the evolutionary periods during which each of 1,433 present human miRNA genes originated within 15 periods, from human to platypus–human common ancestral branch and a class “conserved beyond theria,” primarily using multiple genome alignments of 38 species, plus the pairwise genome alignments of five species. The results showed two peak periods in which the human miRNA genes originated at significantly accelerated rates. The most accelerated rate appeared in the period of the initial phase of hominoid lineage, and the second appeared shortly before Laurasiatherian divergence. Approximately 53% of the present human miRNA genes have originated within the simian lineage to human. In particular, approximately 28% originated within the hominoid lineage. The early phase of placental mammal radiation comprises approximately 28%, while no more than 15% of human miRNAs have been conserved beyond placental mammals. We also clearly showed a general trend, in which the miRNA expression level decreases as the miRNA becomes younger. Intriguingly, amid this decreasing trend of expression, we found one significant rise in the expression level that corresponded to the initial phase of the hominoid lineage, suggesting that increased functional acquisitions of miRNAs originated at this particular period.
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影响因子：
14.9
作者：
Kozomara A;Griffiths-Jones S
通讯作者：
Griffiths-Jones S
影响因子：
1.8
作者：
HOFACKER, IL;FONTANA, W;SCHUSTER, P
通讯作者：
SCHUSTER, P
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30.8
作者：
Bentwich, I;Avniel, A;Bentwich, Z
通讯作者：
Bentwich, Z
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7
作者：
Siepel, A;Bejerano, G;Haussler, D
通讯作者：
Haussler, D
影响因子：
9.5
作者：
Hubisz, Melissa J.;Pollard, Katherine S.;Siepel, Adam
通讯作者：
Siepel, Adam