High Percentage of Isomeric Human MicroRNA and Their Analytical Challenges

Abstract

MicroRNA (miR) are short non-coding RNAs known to post-transcriptionally regulate gene expression, and have been reported as biomarkers for various diseases. miR have also been served as potential drug targets. The identity, functions and detection of a specific miR are determined by its RNA sequence, whose composition is made up of only 4 canonical ribonucleotides. Hence, among over two thousand human miR, their nucleotide compositions are expected to be similar but the extent of similarity has not been reported. In this study, the sequences of mature human miR were downloaded from miRBase, and collated using different tools to determine and compare their nucleotide compositions and sequences. 55% of all human miR were found to be structural isomers. The structural isomers of miR (SimiR) are defined as having the same size and identical nucleotide composition. A number of SimiR were also found to have high sequence similarities. To investigate the extent of SimiR in biological samples, three disease models were chosen, and disease-associated miR were identified from miR2Disease. Among the disease models, as high as 73% of miR were found to be SimiR. This report provides the missing information about human miR and highlights the challenges on the detection of SimiR.

MicroRNA MultiTool: A Software for Identifying Modified and Unmodified Human microRNA Using Mass Spectrometry

“…Due to the short nature of miRNAs, isobaric miRNAs (i.e., miRNAs with different RNA sequences but identical molecular masses) do exist. We recently showed that 55% of all human miRNA are structural isomers [ 28 ]. Under these circumstances, MicroRNA Multitool can be used to narrow down the identity of isobaric miRNA by returning a list of all the isobaric miRNA with the queried mass.…”

“…This is also true when using MicroRNA MultiTool; however, in other cases where multiply charged ions are observed (such as in electrospray ionization MS), the spectra should be deconvoluted to the singly charged ions. Based on one of our recent publications, isomeric human miRNA which have identical molecular mass may exist in the same biological sample [ 28 ]. When mass spectrometry is used to analyze such biological sample, tandem mass spectrometric measurement can be used to differentiate and identify specific isomeric miRNA.…”