The sequence structures of human microRNA molecules and their implications.
The sequence structures of human microRNA molecules and their implications.
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DOI：
10.1371/journal.pone.0054215
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Zhang K
中科院分区：
文献类型：
--
作者：
Fang Z;Du R;Edwards A;Flemington EK;Zhang K
克隆的短基因组序列中的核苷酸计数已经成为将这样的序列注释为miRNA分子的重要标准。虽然大多数人类成熟miRNA序列由22个核苷酸组成，但miRNA序列的特征长度存在差异。也缺乏对这种长度分布以及与这种长度有关或可能影响这种长度的生物因素的系统研究。在本文中，我们打算填补这一空白，调查人类miRNA分子的序列结构，使用统计工具。我们证明了传统的离散概率分布不能很好地模拟人类成熟miRNAs的长度分布，并且我们获得了具有良好拟合的统计分布模型。我们观察到miRNA序列中的四个核苷酸碱基不是随机分布的，这意味着可能存在诸如二核苷酸（三核苷酸或更高级）等可能的结构模式。此外，我们还研究了这种长度分布与多个重要因素的关系，如进化保守性、肿瘤发生、前体环结构的长度和预测靶点的数量。还提出了miRNA序列长度与相应预测基因中靶位点计数分布之间的关联。这项研究产生了几个值得进一步研究的新发现，包括：（1）快速进化引入了miRNA序列长度分布的变化;（2）具有极端序列长度的miRNA不太可能与癌症相关;（3）miRNA序列长度与前体长度和预测靶基因的数量呈正相关。
The count of the nucleotides in a cloned, short genomic sequence has become an important criterion to annotate such a sequence as a miRNA molecule. While the majority of human mature miRNA sequences consist of 22 nucleotides, there exists discrepancy in the characteristic lengths of the miRNA sequences. There is also a lack of systematic studies on such length distribution and on the biological factors that are related to or may affect this length. In this paper, we intend to fill this gap by investigating the sequence structure of human miRNA molecules using statistics tools. We demonstrate that the traditional discrete probability distributions do not model the length distribution of the human mature miRNAs well, and we obtain the statistical distribution model with a decent fit. We observe that the four nucleotide bases in a miRNA sequence are not randomly distributed, implying that possible structural patterns such as dinucleotide (trinucleotide or higher order) may exist. Furthermore, we study the relationships of this length distribution to multiple important factors such as evolutionary conservation, tumorigenesis, the length of precursor loop structures, and the number of predicted targets. The association between the miRNA sequence length and the distributions of target site counts in corresponding predicted genes is also presented. This study results in several novel findings worthy of further investigation that include: (1) rapid evolution introduces variation to the miRNA sequence length distribution; (2) miRNAs with extreme sequence lengths are unlikely to be cancer-related; and (3) the miRNA sequence length is positively correlated to the precursor length and the number of predicted target genes.
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影响因子：
14.9
作者：
Kozomara A;Griffiths-Jones S
通讯作者：
Griffiths-Jones S
DOI：
10.1093/bioinformatics/btr149
发表时间：
2011-05-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Ellwanger DC;Büttner FA;Mewes HW;Stümpflen V
通讯作者：
Stümpflen V
影响因子：
14.9
作者：
Griffiths-Jones, S
通讯作者：
Griffiths-Jones, S
Mirbase：MicroRNA基因组学的工具。
影响因子：
14.9
作者：
Griffiths-Jones, Sam;Saini, Harpreet Kaur;van Dongen, Stijn;Enright, Anton J.
通讯作者：
Enright, Anton J.
影响因子：
14.9
作者：
Griffiths-Jones S;Grocock RJ;van Dongen S;Bateman A;Enright AJ
通讯作者：
Enright AJ