Translational regulation by non-protein-coding RNAs: different targets, common themes

Incomplete penetrance and variable expressivity: is there a microRNA connection?

Incomplete penetrance and variable expressivity are non-Mendelian phenomena resulting in the lack of correlation between genotype and phenotype. Not withstanding the diversity in mechanisms, differential expression of homologous alleles within cells manifests as variations in penetrance and expressivity of mutations between individuals of the same genotype. These phenomena are seen most often in dominantly inherited diseases, implying that they are sensitive to concentration of the gene product. In this framework and the advances in understanding the role of microRNA (miRNA) in fine-tuning gene expression at translational level, we propose miRNA-mediated regulation as a mechanism for incomplete penetrance and variable expressivity. The presence of miRNA binding sites at 3' UTR, co-expression of target gene-miRNA pairs for genes showing incomplete penetrance and variable expressivity derived from available data lend support to our hypothesis. Single nucleotide polymorphisms in the miRNA target site facilitate the implied differential targeting of the transcripts from homologous alleles.

Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis

BACKGROUND

MicroRNAs (miRNAs) have critical functions in various biological processes. MiRNA profiling is an important tool for the identification of differentially expressed miRNAs in normal cellular and disease processes. A technical challenge remains for high-throughput miRNA expression analysis as the number of miRNAs continues to increase with in silico prediction and experimental verification. Our study critically evaluated the performance of a novel miRNA expression profiling approach, quantitative RT-PCR array (qPCR-array), compared to miRNA detection with oligonucleotide microchip (microarray).

RESULTS

High reproducibility with qPCR-array was demonstrated by comparing replicate results from the same RNA sample. Pre-amplification of the miRNA cDNA improved sensitivity of the qPCR-array and increased the number of detectable miRNAs. Furthermore, the relative expression levels of miRNAs were maintained after pre-amplification. When the performance of qPCR-array and microarrays were compared using different aliquots of the same RNA, a low correlation between the two methods (r=-0.443) indicated considerable variability between the two assay platforms. Higher variation between replicates was observed in miRNAs with low expression in both assays. Finally, a higher false positive rate of differential miRNA expression was observed using the microarray compared to the qPCR-array.

CONCLUSION

Our studies demonstrated high reproducibility of TaqMan qPCR-array. Comparison between different reverse transcription reactions and qPCR-arrays performed on different days indicated that reverse transcription reactions did not introduce significant variation in the results. The use of cDNA pre-amplification increased the sensitivity of miRNA detection. Although there was variability associated with pre-amplification in low abundance miRNAs, the latter did not involve any systemic bias in the estimation of miRNA expression. Comparison between microarray and qPCR-array indicated superior sensitivity and specificity of qPCR-array.

The molecular machines that mediate microRNA maturation

MicroRNAs (miRNA) are small RNAs that regulate the translation of thousands of message RNAs and play a profound role in mammalian biology. Over the past 5 years, significant advances have been made towards understanding the pathways that generate miRNAs and the mechanisms by which miRNAs exert their regulatory functions. An emerging theme is that miRNAs are both generated by and utilized by large and complex macromolecular assemblies. Here, we review the biology of mammalian miRNAs with a focus on the macromolecular complexes that generate and control the biogenesis of miRNAs.