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

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

• Research Articles • Previous Articles Next Articles

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

Abstract

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

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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Prediction and functional analysis of lincRNAs targeted by miRNAs

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