ReviewDiscriminating RNA variants with single-molecule allele-specific FISH

DNA mutations of various types often affect the cellular localization and function of gene products. The role of mutant transcripts in the pathogenesis of human disease is increasingly recognized. Among the pathogenic RNA variants are transcripts with single nucleotide substitutions, small insertions or deletions, aberrantly or alternatively spliced transcripts and RNAs derived from fused genes. To discriminate among transcripts, particularly those of low abundance, showing small or large sequence differences, a highly sensitive and specific RNA imaging method is required. The method that fulfills these criteria is single-molecule fluorescence in situ hybridization (smFISH) combined with probes discriminating among RNA variants. With this method, RNA transcripts produced from individual alleles can be imaged, and differences in their transcription, processing, cellular localization and decay can be revealed. In addition to its applications for studying physiological processes involving RNA variants, smFISH offers several advantages for disease related mutation research. Further development of allele-specific microscopic methods may broaden group of RNA variants analyzed, including RNAs with expanded repeat tract, different variants of 3′UTR, RNAs differing in length of polyA tract or transcripts produced from alternative start codons. Moreover, first attempts for allele-specific RNA live imaging were made adding time-lapse analysis. In this review, we discuss important aspects of the variant-specific smFISH methodology and present examples of its applications in deciphering RNA-mediated pathogenic mechanisms in a variety of human diseases, including cancer, neurological, immunological and cardiovascular diseases.