TITLE

Limited evidence for evolutionarily conserved targeting of long non-coding RNAs by microRNAs

AUTHOR(S)
Alaei-Mahabadi, Babak; Larsson, Erik
PUB. DATE
September 2013
SOURCE
Silence;2013, Vol. 4 Issue 1, p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Long non-coding RNAs (lncRNAs) are emerging as important regulators of cell physiology, but it is yet unknown to what extent lncRNAs have evolved to be targeted by microRNAs. Comparative genomics has previously revealed widespread evolutionarily conserved microRNA targeting of protein-coding mRNAs, and here we applied a similar approach to lncRNAs. Findings: We used a map of putative microRNA target sites in lncRNAs where site conservation was evaluated based on 46 vertebrate species. We compared observed target site frequencies to those obtained with a random model, at variable prediction stringencies. While conserved sites were not present above random expectation in intergenic lncRNAs overall, we observed a marginal over-representation of highly conserved 8-mer sites in a small subset of cytoplasmic lncRNAs (12 sites in 8 lncRNAs at 56% false discovery rate, P = 0.10). Conclusions: Evolutionary conservation in lncRNAs is generally low but patch-wise high, and these patches could, in principle, harbor conserved target sites. However, while our analysis efficiently detected conserved targeting of mRNAs, it provided only limited and marginally significant support for conserved microRNA-lncRNA interactions. We conclude that conserved microRNA-lncRNA interactions could not be reliably detected with our methodology.
ACCESSION #
90260331

 

Related Articles

  • Inferring Potential microRNA-microRNA Associations Based on Targeting Propensity and Connectivity in the Context of Protein Interaction Network. Sun, Jie; Zhou, Meng; Yang, Haixiu; Deng, Jiaen; Wang, Letian; Wang, Qianghu // PLoS ONE;Jul2013, Vol. 8 Issue 7, p1 

    MicroRNAs (miRNAs) are a group of small non-coding RNAs that play important regulatory roles at the post-transcriptional level. Although several computational methods have been developed to compare miRNAs, it is still a challenging and a badly needed task with the availability of various...

  • lnCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA. Das, Shaoli; Ghosal, Suman; Sen, Rituparno; Chakrabarti, Jayprokas // PLoS ONE;Jun2014, Vol. 9 Issue 6, p1 

    Long noncoding RNA (lncRNA) influences post-transcriptional regulation by interfering with the microRNA (miRNA) pathways, acting as competing endogenous RNA (ceRNA). These lncRNAs have miRNA responsive elements (MRE) in them, and control endogenous miRNAs available for binding with their target...

  • Long Noncoding RNA MEG3 Interacts with p53 Protein and Regulates Partial p53 Target Genes in Hepatoma Cells. Zhu, Juanjuan; Liu, Shanshan; Ye, Fuqiang; Shen, Yuan; Tie, Yi; Zhu, Jie; Wei, Lixin; Jin, Yinghua; Fu, Hanjiang; Wu, Yongge; Zheng, Xiaofei // PLoS ONE;10/7/2015, Vol. 10 Issue 10, p1 

    Maternally Expressed Gene 3 (MEG3) encodes a lncRNA which is suggested to function as a tumor suppressor. Previous studies suggested that MEG3 functioned through activation of p53, however, the functional properties of MEG3 remain obscure and their relevance to human diseases is under continuous...

  • Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs. Chiang, Kevin; Shu, Jiang; Zempleni, Janos; Cui, Juan // PLoS ONE;Jun2015, Vol. 10 Issue 6, p1 

    With the advent of high throughput technology, a huge amount of microRNA information has been added to the growing body of knowledge for non-coding RNAs. Here we present the Dietary MicroRNA Databases (DMD), the first repository for archiving and analyzing the published and novel microRNAs...

  • Large non-coding RNA in pluripotency. Le Bot, Nathalie // Nature Cell Biology;May2013, Vol. 15 Issue 5, p449 

    The article presents a study by Liu and colleagues which showed that linc-RoR, a big non-coding RNA, increases pluripotency factors in embryonic stem cells (ESCs) and keeps microRNAs away from their target sites.

  • Novel roles of non-coding brain RNAs in health and disease. Soreq, Hermona // Frontiers in Molecular Neuroscience;Jun2014, Vol. 7, p1 

    An introduction is presented which outlines the theme of the issue focusing on non-coding RNA and microRNA research.

  • miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Jeggari, Ashwini; Marks, Debora S; Larsson, Erik // Bioinformatics;8/1/2012, Vol. 28 Issue 15, p2062 

    Summary: Although small non-coding RNAs, such as microRNAs, have well-established functions in the cell, long non-coding RNAs (lncRNAs) have only recently started to emerge as abundant regulators of cell physiology, and their functions may be diverse. A small number of studies describe...

  • Argonaute proteins: functional insights and emerging roles. Meister, Gunter // Nature Reviews Genetics;Jul2013, Vol. 14 Issue 7, p447 

    Small-RNA-guided gene regulation has emerged as one of the fundamental principles in cell function, and the major protein players in this process are members of the Argonaute protein family. Argonaute proteins are highly specialized binding modules that accommodate the small RNA component - such...

  • The physiological and pathophysiological roles of adipocyte miRNAs. Ling, Hongyan; Li, Xing; Yao, Chao Hua; Hu, Bi; Liao, Duanfang; Feng, Shuidong; Wen, Gebo; Zhang, Liang // Biochemistry & Cell Biology;Aug2013, Vol. 91 Issue 4, p195 

    MicroRNAs (miRNAs) are highly conserved, small, noncoding RNAs that regulate gene expression at the posttranscriptional level. Their actions affect numerous important biological processes, including adipocyte differentiation and function, sugar and lipid metabolism, and insulin production and...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics