Trends in Biotechnology
Volume 26, Issue 2, February 2008, Pages 70-76
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Review
Profiling microRNA expression with microarrays

https://doi.org/10.1016/j.tibtech.2007.11.007Get rights and content

The discovery of several types of small RNAs (sRNAs) has led to a steady increase in available RNA databases. Many of these sRNAs remain to be validated and functionally characterized. Recent advances in microRNA (miRNA)-expression profiling of different tissues, stages of development and physiological or pathological states are beginning to be explored using several technological approaches. In this review, these recent advances in miRNA microarray technology and their applications, particularly in basic research and clinical diagnosis, will be summarized and discussed. The methods for miRNA enrichment and probe design and labeling will also be discussed with an emphasis on evaluation of predicted miRNA sequences, analysis of miRNA expression and exploration of the potential roles of miRNA sequences in the regulation of stem cell differentiation and tissue- and time-specific profiling patterns of their target genes.

Introduction

Small RNAs (sRNAs) are a growing class of recently identified endogenous non-protein-coding sRNAs (ncRNAs) 21–35 nucleotides in length. They can be divided into at least six types, including microRNAs (miRNAs), tiny non-coding RNAs (tncRNAs), small interfering RNAs (siRNAs), repeat-associated small interfering RNAs (rasiRNAs), small modulatory RNAs (smRNAs) and Piwi (P-element-induced wimpy testis)-interacting RNAs (piRNA) 1, 2. The miRNAs have been most widely studied [3] and are derived from introns or extrons of protein-coding and non-coding genes – hundreds of miRNAs have been cloned and sequenced 4, 5. Bioinformatics and genetic analysis suggest that these unique miRNA genes are present in the genomes of mouse, humans, Drosophila, Caenorhabditis elegans, Arabidopsis, viruses and fungi and that they are expressed in a regulated manner. Several investigations have demonstrated that miRNAs serve as guide molecules, in that they form base pairs with partially or fully complementary sequences in target mRNAs leading to translational repression and/or mRNA cleavage 6, 7. Moreover, miRNAs have been shown to induce transcriptional silencing, resulting in the modification of DNA and/or chromatin in yeast, plants and animals 8, 9, 10, 11, 12, 13. They can also potentially regulate hundreds of mRNAs. Some miRNAs have been shown to affect stem cell differentiation, organ development, cell death, phase change, signaling, disease, cancer and the response to biotic and abiotic environmental stresses 3, 14, 15, 16. Furthermore, many miRNAs are highly conserved in animals and plants. They have been shown to have unique tissue-specific, developmental stage-specific or disease-specific patterns. These observations imply that each tissue is characterized by a specific set of miRNAs that might be defining features of that tissue [3].

The advent of genomics and the burgeoning amount of genomics data have greatly accelerated studies on structure and function of genes, and significantly altered our understanding of gene regulation. Undoubtedly, microarrays have made important contributions to both basic and applied research, and have the potential to change the practice of medicine to a more personalized endeavor 17, 18, 19, 20. The goal and power of microarray experiments is to survey patterns of mRNA expression by assaying the expression levels of hundreds to thousands of genes in a single assay. However, the profiling of miRNA expression is a relatively new field. Several parameters, including their small size, low abundance and the tissue-, developmental stage- and disease state- specificities in miRNA expression, make the adaptation of array technology to the analysis of miRNA expression challenging [21]. Nevertheless, several methodologies have been adapted for profiling miRNA expression. They include northern blotting with radiolabeled probes 22, 23, cloning [24], quantitative PCR-based amplification of precursor or mature miRNAs 25, 26, serial analysis of gene expression (SAGE)-based techniques [27], bead-based profiling methods 28, 29 and oligonucleotide microarrays 30, 21, 31. Several studies demonstrated that miRNA microarrays succeeded in assessing miRNA expression on a global scale and enabled analysis of the expression of hundreds of miRNA genes in a single experiment. miRNA arrays are now being developed to explore the biogenesis of miRNAs, tissue distribution, differential miRNA expression between normal and abnormal states, disease characterization, stem cell development, pathway mapping, mechanisms of action and tumorigenesis 32, 33, 34. Moreover, scientists are also conducting profiling studies that might lead to the use of small RNA arrays in molecular diagnosis of disease and in evaluation of drug efficacy and toxicity. This review attempts to focus on the sRNA array technologies and their application in basic and clinical research related to the sRNA ‘world’ (which includes all types of sRNA with lengths of less than 40 nt).

Section snippets

miRNA microarrays

In contrast to mRNA profiling technologies, miRNA profiling must take into account the difference between mature miRNAs and their precursors, and should also distinguish between miRNAs that differ by as little as a single nucleotide [35]. Moreover, it has been shown that the sequences of mature miRNAs display unequal melting temperatures. These features – specific for miRNAs, present major challenges for sample labeling and microarray probe design. The following section gives critical

Application of miRNA arrays

miRNA microarrays have been successfully used for the primary identification of new miRNAs that were predicted by bioinformatics approaches, for the dissection of differential expression of different miRNAs in the same cells, and for the comparison of miRNA expression profiles from different tissues or cells. These arrays have also been used for evaluating miRNA expression during development, differentiation, oncogenesis and other disease processes. In the following section we briefly describe

Concluding remarks

Widespread and comprehensive use of miRNA microrrays will enable the identification of novel classes of sRNAs, quantification of miRNA expression and detection of miRNA expression patterns within and across species. Moreover, miRNA arrays can identify the expression of several hundred genes in the same sample at once while requiring only small amounts of total RNA. miRNA arrays will therefore increasingly contribute to both basic and applied research and promise to change the practice of

Acknowledgements

This work was supported by the Chinese Academy of Sciences’ ‘Hundred Talents Program’ and the 863 program (grant number 2006AA02Z131 to J.Q.Y). We apologize to colleagues whose work was not mentioned owing to space constraints.

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