After 12 years from its first application, microarray technology has become the reference technique to monitor gene expression of thousands of genes in the same experiment. In the past few years an increasing amount of evidence showed the importance of non coding RNA (ncRNA) in different human diseases. The microRNAs (miRNAs) are one of the groups of ncRNA. They are small RNA fragments, 19-25 nucleotides long, with a main regulatory function on both protein coding genes and non-coding RNAs. The application of microarray platforms applied to miRNA profiling determined their deregulation in virtually all human diseases that have been studied. We previously developed a custom miRNA microarray platform, and here we describe the protocol we used to work with it including the oligo design strategy, the microaray printing protocol, the target-probe hybridization and the signal detection.
Protein-coding genes versus non-coding RNAAlthough 5% of the human genome evolves under purifying selection, only 2% of this set is represented by protein coding RNA (i.e. protein coding genes) (1). The remaining 3% is split into non-genic DNA and non-coding RNA (2, 3). The main differences between protein coding and non-coding RNA (mRNA and ncRNA respectively) is based on the absence of any Open Reading Frame (ORF) for ncRNA and on the difficulty to predict the transcript of ncRNA from its genomic structure (4). The ncRNA family is heterogeneous, based on the different size of the product (from few nucleotides to thousands) and on its function. NcRNA can have a generic function such as ribosomal RNA (rRNA) and transfer RNA (tRNA), both involved in mRNA/protein translation, or small nuclear RNA (snRNA) involved in splicing, and finally small nucleolar RNA (snoRNA) involved in the modification of rRNA. The last members of the ncRNA to be discovered are involved in post-transcriptionally regulating protein expression through small RNA molecules such as small interference RNA (siRNA) (5) and microRNA (miRNA) (6-8).
Different approaches to quantify tiny RNA moleculesThe mature miRNAs are very small RNAs, 19-25 nucleotides (nt) long and because of this small size there are differences in the approaches to quantify miRNAs and mRNAs. For Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
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Author ManuscriptMethods. Author manuscript; available in PMC 2012 April 9. On the other hand, in our experience the miRNAs seems to be more stable than longer RNAs, for example in degraded samples it is still possible to obtain readable miRNA expression data. Moreover other groups reported a hi...