High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes.
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes.
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DOI：
10.1371/journal.pone.0000219
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发表时间：
2007-02-14
期刊：
影响因子：
3.7
通讯作者：
Carrington JC
中科院分区：
文献类型：
--
作者：
Fahlgren N;Howell MD;Kasschau KD;Chapman EJ;Sullivan CM;Cumbie JS;Givan SA;Law TF;Grant SR;Dangl JL;Carrington JC
在植物中，微小RNA（miRNAs）是两类小RNA中的一类，主要在转录后水平作为负调控因子发挥作用。植物界的一些MIRNA基因很古老，其保守性在被子植物和苔藓植物之间都存在，而其他许多则是近期进化而来的。在此，我们利用深度测序和计算方法来鉴定、分析拟南芥中不保守的MIRNA基因并对其进行图谱绘制。我们鉴定出了48个不保守的MIRNA家族，几乎所有家族都由单个基因代表。对miRNA前体发夹臂的序列相似性分析揭示了16个MIRNA基因座通过蛋白质编码基因序列的反向重复事件近期进化起源的证据。有趣的是，这些近期进化的MIRNA基因走了不同的路径。一些不保守的miRNAs与提供亲本序列的基因家族的靶转录本相互作用并对其进行调控，而其他的则已经偏离到与亲本基因家族转录本不相互作用的程度。一些年轻的MIRNA基因座明显起源于一个基因家族，但形成的miRNAs却靶向另一个家族的转录本。我们认为MIRNA基因正在经历相对频繁的产生和消亡，只有一部分通过整合到调控网络中而稳定下来。
In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several MIRNA genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep sequencing and computational methods to identify, profile and analyze non-conserved MIRNA genes in Arabidopsis thaliana. 48 non-conserved MIRNA families, nearly all of which were represented by single genes, were identified. Sequence similarity analyses of miRNA precursor foldback arms revealed evidence for recent evolutionary origin of 16 MIRNA loci through inverted duplication events from protein-coding gene sequences. Interestingly, these recently evolved MIRNA genes have taken distinct paths. Whereas some non-conserved miRNAs interact with and regulate target transcripts from gene families that donated parental sequences, others have drifted to the point of non-interaction with parental gene family transcripts. Some young MIRNA loci clearly originated from one gene family but form miRNAs that target transcripts in another family. We suggest that MIRNA genes are undergoing relatively frequent birth and death, with only a subset being stabilized by integration into regulatory networks.
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