Dataset Information

Genome-wide identification of miRNA targets by PAR-CLIP.

ABSTRACT: miRNAs are short (20-23 nt) RNAs that are loaded into proteins of the Argonaute (AGO) family and guide them to partially complementary target sites on mRNAs, resulting in mRNA destabilization and/or translational repression. It is estimated that about 60% of the mammalian genes are potentially regulated by miRNAs, and therefore methods for experimental miRNA target determination have become valuable tools for the characterization of posttranscriptional gene regulation. Here we present a step-by-step protocol and guidelines for the computational analysis for the large-scale identification of miRNA target sites in cultured cells by photoactivatable ribonucleoside enhanced crosslinking and immunoprecipitation (PAR-CLIP) of AGO proteins.

SUBMITTER: Hafner M

PROVIDER: S-EPMC3508682 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature

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Genome-wide identification of miRNA targets by PAR-CLIP.

Hafner Markus M Lianoglou Steve S Tuschl Thomas T Betel Doron D

Methods (San Diego, Calif.) 20120819 2

miRNAs are short (20-23 nt) RNAs that are loaded into proteins of the Argonaute (AGO) family and guide them to partially complementary target sites on mRNAs, resulting in mRNA destabilization and/or translational repression. It is estimated that about 60% of the mammalian genes are potentially regulated by miRNAs, and therefore methods for experimental miRNA target determination have become valuable tools for the characterization of posttranscriptional gene regulation. Here we present a step-by- ...[more]

PMID: 22926237

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Project description:Long intergenic noncoding RNAs (lincRNAs) are endogenous non-coding RNAs (ncRNAs) that are transcribed from 'intergenic' regions of the genome and may play critical roles in regulating gene expression through multiple RNA-mediated mechanisms. MicroRNAs (miRNAs) are single-stranded small ncRNAs of approximately 21-24 nucleotide (nt) that are involved in transcriptional and post-transcriptional gene regulation. While miRNAs functioning as mRNA repressors have been studied in detail, the influence of miRNAs on lincRNAs has seldom been investigated in plants.LincRNAs as miRNA targets or decoys were predicted via GSTAr.pl script with a set of rules, and lincRNAs as miRNA targets were validated by degradome data. Conservation analysis of lincRNAs as miRNA targets or decoys were conducted using BLASTN and MAFFT. The function of lincRNAs as miRNA targets were predicted via a lincRNA-mRNA co-expression network, and the function of lincRNAs as miRNA decoys were predicted according to the competing endogenous RNA (ceRNA) hypothesis.In this work, we developed a computational method and systematically predicted 466 lincRNAs as 165 miRNA targets and 86 lincRNAs as 58 miRNA decoys in maize (Zea mays L.). Furthermore, 34 lincRNAs predicted as 33 miRNA targets were validated based on degradome data. We found that lincRNAs acting as miRNA targets or decoys are a common phenomenon, which indicates that the regulated networks of miRNAs also involve lincRNAs. To elucidate the function of lincRNAs, we reconstructed a miRNA-regulated network involving 78 miRNAs, 117 lincRNAs and 8834 mRNAs. Based on the lincRNA-mRNA co-expression network and the competing endogenous RNA hypothesis, we predicted that 34 lincRNAs that function as miRNA targets and 86 lincRNAs that function as miRNA decoys participate in cellular and metabolic processes, and play role in catalytic activity and molecular binding functions.This work provides a comprehensive view of miRNA-regulated networks and indicates that lincRNAs can participate in a layer of regulatory interactions as miRNA targets or decoys in plants, which will enable in-depth functional analysis of lincRNAs.

Dataset Information

Genome-wide identification of miRNA targets by PAR-CLIP.

Publications

Genome-wide identification of miRNA targets by PAR-CLIP.

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