Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana.
Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana.
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DOI：
10.1093/nar/gkp272
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发表时间：
2009-07
影响因子：
14.9
通讯作者：
Merkle T
中科院分区：
文献类型：
--
作者：
Alves L Jr;Niemeier S;Hauenschild A;Rehmsmeier M;Merkle T
微小RNA（microRNAs，miRNAs）是一类长度为20-24 nt的内源性非编码RNA，在后生动物和植物中起转录后调节作用。植物miRNA靶标通常含有与miRNA具有近乎完美互补性的单个序列基序。在这里，我们扩展和应用程序RNAhybrid，以确定新的miRNA目标在完整的注释拟南芥转录组。RNAhybrid预测能量上最有利的miRNA：mRNA杂交体，其与用户定义的结构约束一致。这些是：（i）从miRNA的5′-末端计数的核苷酸8至12的双链体的完美碱基配对;（ii）任一链中最大长度为一个核苷酸的环;（iii）大小不超过一个核苷酸的凸起;和（iv）不超过两个核苷酸的未配对末端突出端。G：U碱基对不被视为错配，但对整体自由能的贡献较不利。根据它们的最小自由能对所得杂交体进行过滤，从而总体预测了600多个新的miRNA靶点。用随机化的miRNA或随机化的靶序列作为阴性对照来评估预测的特异性和信噪比。我们的研究结果与最近的观察结果一致，即大多数miRNA靶点不是转录因子。
MicroRNAs (miRNAs) are 20–24 nt long endogenous non-coding RNAs that act as post-transcriptional regulators in metazoa and plants. Plant miRNA targets typically contain a single sequence motif with near-perfect complementarity to the miRNA. Here, we extended and applied the program RNAhybrid to identify novel miRNA targets in the complete annotated Arabidopsis thaliana transcriptome. RNAhybrid predicts the energetically most favorable miRNA:mRNA hybrids that are consistent with user-defined structural constraints. These were: (i) perfect base pairing of the duplex from nucleotide 8 to 12 counting from the 5′-end of the miRNA; (ii) loops with a maximum length of one nucleotide in either strand; (iii) bulges with no more than one nucleotide in size; and (iv) unpaired end overhangs not longer than two nucleotides. G:U base pairs are not treated as mismatches, but contribute less favorable to the overall free energy. The resulting hybrids were filtered according to their minimum free energy, resulting in an overall prediction of more than 600 novel miRNA targets. The specificity and signal-to-noise ratio of the prediction was assessed with either randomized miRNAs or randomized target sequences as negative controls. Our results are in line with recent observations that the majority of miRNA targets are not transcription factors.
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