Advances in the techniques for the prediction of microRNA targets.

Hao Zheng,Shi-Wen Jiang,Qinyou Liu,Jin-Tao Wang,Rongguo Fu,Haibin Chen

doi:10.3390/ijms14048179

Abstract

MicroRNAs (miRNAs) are small, non-coding, endogenous RNA molecules that play important roles in a variety of normal and diseased biological processes by post-transcriptionally regulating the expression of target genes. They can bind to target messenger RNA (mRNA) transcripts of protein-coding genes and negatively control their translation or cause mRNA degradation. miRNAs have been found to actively regulate a variety of cellular processes, including cell proliferation, death, and metabolism. Therefore, their study is crucial for the better understanding of cellular functions in eukaryotes. To better understand the mechanisms of miRNA: mRNA interaction and their cellular functions, it is important to identify the miRNA targets accurately. In this paper, we provide a brief review for the advances in the animal miRNA target prediction methods and available resources to facilitate further study of miRNAs and their functions.

Highlights

In addition to DNA methylation and histone modification, epigenetic mechanisms have recently been extended to microRNAs, which are important regulators of gene expression in many biological systems. miRNAs are small, non-coding, endogenous RNA molecules, about 19–24 nucleotides in length that can negatively control their target gene expression post-transcriptionally [1].This is mainly achieved by recognizing and binding to the 3' untranslated region of the target messenger RNA sequences [2]. miRNAs have been found to actively regulate a variety of cellular processes, including cell proliferation, death, and metabolism, and their study is crucial for the better understanding of cellular functions in eukaryotes [3].Mature miRNAs are incorporated into the RNA-induced silencing complex (RISC), where miRNAs interact with target mRNAs
A key step in the identification of miRNA target is the selection of features that are potentially of predictive power
By identifying mRNAs with strong base pairing to the 5' region of the miRNA and evaluating the number and quality of these complementary sites, Lewis et al identified more than 400 regulatory target genes for the conserved vertebrate miRNAs [7]

Summary

Introduction

In addition to DNA methylation and histone modification, epigenetic mechanisms have recently been extended to microRNAs (miRNAs), which are important regulators of gene expression in many biological systems. miRNAs are small, non-coding, endogenous RNA molecules, about 19–24 nucleotides in length that can negatively control their target gene expression post-transcriptionally [1]. MiRNAs are small, non-coding, endogenous RNA molecules, about 19–24 nucleotides in length that can negatively control their target gene expression post-transcriptionally [1]. This is mainly achieved by recognizing and binding to the 3' untranslated region of the target messenger RNA (mRNA) sequences [2]. Mature miRNAs are incorporated into the RNA-induced silencing complex (RISC), where miRNAs interact with target mRNAs. Approximately one thousand miRNAs have been discovered in humans and are believed to control more than half of the protein coding genes, where a single miRNAs might regulate hundreds of such genes [4]. The readers are referred to the literature cited in this review, and the references therein for further details

Methods for miRNA Target Recognition

Resources for miRNA Target Prediction

Next-Generation Sequencing for miRNA Target Identification

Future Work

Findings

Conflict of Interest