miRNAs调控lincRNAs的生物信息学预测与功能分析

doi:10.3724/SP.J.1005.2014.1226

遗传 ›› 2014, Vol. 36 ›› Issue (12): 1226-1234.doi: 10.3724/SP.J.1005.2014.1226

miRNAs调控lincRNAs的生物信息学预测与功能分析

樊春燕, 魏强, 郝志强, 李广林

陕西师范大学生命科学学院, 西安 710062

收稿日期:2014-05-21 出版日期:2014-12-20 发布日期:2014-12-20
通讯作者: 李广林, 博士, 副教授, 研究方向：功能基因组学与生物信息学。E-mail: glli@snnu.edu.cn E-mail:cyfan89@163.com
作者简介:樊春燕, 硕士研究生, 专业方向：非编码RNA。Tel: 15829008925;
基金资助:
教育部新世纪优秀人才支持计划(编号：NCET-12-0896), 陕西省自然科学基础研究计划项目(编号：2014JM3074)和陕西师范大学研究生培养创新基金项目(编号：2013CXS020)资助

Prediction and functional analysis of lincRNAs targeted by miRNAs

Chunyan Fan, Qiang Wei, Zhiqiang Hao, Guanglin Li

College of Life Science, Shaanxi Normal University, Xi’an 710062, China

Received:2014-05-21 Online:2014-12-20 Published:2014-12-20

摘要/Abstract

摘要： 基因间长链非编码RNAs(Long intergenic non-coding RNAs, lincRNAs)是位于蛋白编码基因之间的长度超过200 nt的非编码RNAs, 在动物中参与细胞周期调控、免疫监视、胚胎干细胞分化等多种生物学过程, 但是lincRNAs在大多数植物中的功能尚不清楚。MicroRNAs(miRNAs)是真核生物中一类在转录水平和转录后水平介导基因沉默的21 nt左右的内源性单链小非编码RNAs分子, 通过序列互补的方式调控靶标基因的表达。目前miRNAs的靶标研究主要集中于编码蛋白的基因, 而对于靶标为非编码RNAs的研究较少, 尤其在植物中的研究更为少见。为了系统挖掘植物中lincRNAs的功能, 文章整合miRNAs数据、cDNAs数据和降解组数据, 利用生物信息学方法找到拟南芥(Arabidopsis thaliana)337个成熟miRNAs在2708个lincRNAs上的可能结合位点, 构建了miRNAs-mRNAs-lincRNAs调控网络, 并根据竞争性内源(ceRNA)假说预测lincRNAs的功能, 为进一步阐明植物中miRNAs对lincRNAs的调控机制以及lincRNAs的功能奠定了基础。

关键词: 微小RNAs, 基因间长链非编码RNAs, 降解组, 靶标

Abstract: Long intergenic non-coding RNAs (lincRNAs) located between protein-coding genes are non-coding RNAs longer than 200 nucleotides in length. LincRNAs are involved in a variety of biological processes such as cell cycle regulation, immune surveillance and embryonic stem cells differentiation in animals; however, the function of lincRNAs in plants is largely unclear. MicroRNAs (miRNAs) are a class of endogenous, single-stranded, non-coding small (~21 nt) RNAs, which can regulate gene expression at transcriptional or post-transcriptional level in eukaryotes by means of sequence complementation. Now, intensive studies on protein-coding genes targeted by miRNAs have been carried out, but the research on non-coding RNAs targeted by miRNAs is seldom explored, especially in plants. In order to uncover the potential function of lincRNAs, the data including miRNAs, cDNAs and degradomes were firstly collected and integrated, followed by bioinformatics methods to predict the potential binding sites of 337 mature miRNAs at 2708 lincRNAs in Arabidopsis thaliana. The regulatory networks of miRNAs-mRNAs-lincRNAs were constructed and the function of lincRNAs was predicted according to the competing endogenous RNA (ceRNA) hypothesis. This study may lay a solid foundation for elucidating the regulatory mechanism of miRNAs on lincRNAs as well as the function of lincRNAs in plants.

Key words: microRNAs (miRNAs), long intergenic non-coding RNAs (lincRNAs), degradome data, targets

樊春燕, 魏强, 郝志强, 李广林. miRNAs调控lincRNAs的生物信息学预测与功能分析[J]. 遗传, 2014, 36(12): 1226-1234.

Chunyan Fan, Qiang Wei, Zhiqiang Hao, Guanglin Li. Prediction and functional analysis of lincRNAs targeted by miRNAs[J]. HEREDITAS(Beijing), 2014, 36(12): 1226-1234.

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miRNAs调控lincRNAs的生物信息学预测与功能分析

Prediction and functional analysis of lincRNAs targeted by miRNAs

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