Tiny giants of gene regulation: experimental strategies for microRNA functional studies

Abstract

The discovery over two decades ago of short regulatory microRNAs (miRNAs) has led to the inception of a vast biomedical research field dedicated to understanding these powerful orchestrators of gene expression. Here we aim to provide a comprehensive overview of the methods and techniques underpinning the experimental pipeline employed for exploratory miRNA studies in animals. Some of the greatest challenges in this field have been uncovering the identity of miRNA–target interactions and deciphering their significance with regard to particular physiological or pathological processes. These endeavors relied almost exclusively on the development of powerful research tools encompassing novel bioinformatics pipelines, high‐throughput target identification platforms, and functional target validation methodologies. Thus, in an unparalleled manner, the biomedical technology revolution unceasingly enhanced and refined our ability to dissect miRNA regulatory networks and understand their roles in vivo in the context of cells and organisms. Recurring motifs of target recognition have led to the creation of a large number of multifactorial bioinformatics analysis platforms, which have proved instrumental in guiding experimental miRNA studies. Subsequently, the need for discovery of miRNA–target binding events in vivo drove the emergence of a slew of high‐throughput multiplex strategies, which now provide a viable prospect for elucidating genome‐wide miRNA–target binding maps in a variety of cell types and tissues. Finally, deciphering the functional relevance of miRNA post‐transcriptional gene silencing under physiological conditions, prompted the evolution of a host of technologies enabling systemic manipulation of miRNA homeostasis as well as high‐precision interference with their direct, endogenous targets. WIREs Dev Biol 2016, 5:311–362. doi: 10.1002/wdev.223For further resources related to this article, please visit the WIREs website.

Overview of microRNA Modulation in Analgesic Research

“…Currently, the human genome is known to generate 2588 mature miRNAs (http://www.mirbase.org). Once miRNAs of interest are identified, online bioinformatics databases can be used to predict potential target genes (M. M. Akhtar, Micolucci, Islam, Olivieri, & Procopio, 2016) and functional target validation can be pursued (Steinkraus, Toegel, & Fulga, 2016). The biological roles of miRNAs are complex.…”

Animal Models to Study MicroRNA Function

“…Advancements in the field have been possible due to state-of-the-art technologies such as high throughput screening and deep sequencing, but majorly due to the development of appropriate in vivo model systems (Review 19 ). Therefore, the focus of this review will be on the various model systems that have been instrumental in elucidating the roles of miRNAs in cancers and the technologies that have been extensively applied to generate these animal model systems.…”

“…Recently there has been a surge in the development of bioinformatic tools to precisely predict targets of a miRNA, or predict miRNAs that target a particular transcript 19 . Several computationally predicated miRNA-target pairs based on complementarity between the miRNA seed sequence and the 3′-UTR of transcripts have been experimentally validated 8,46,60,67,85–87 .…”

sta-1is repressed bymir-58family inCaenorhabditis elegans

“…Most microRNA-target interactions are merely suggested through genome-wide studies, which involve the analyses of transcriptomes or proteomes physically associated to microRNAs 1 . These studies are essential for outlining networks of putative interactions between miRNAs and their target genes.…”