A novel method for the identification and quantification of N6-methyladenosine motifs in RNA transcripts

Abstract

N6-methyladenosine profiles of mRNA transcripts regulate their translocation from the nucleus to the cytosol, stability, and translational efficiency; hence, they have been implicated in gene expression and disease progression. The m6A-methylation is widely associated with various cancers and neurological, cardiovascular, and developmental disorders, which demand early diagnosis. A robust m6A-motif prediction is necessary to enable us to identify the regulatory nucleic acid sequences that determine mRNA fate in normal and diseased conditions. We have developed a transcript-aware computational pipeline, termed m6AFunctional Index in Transcription (m6A-FINDiT), that can identify potential m6A sites on mRNA transcripts, considering molecular intricacies associated with their secondary structure. This tool can separately identify m6A motifs within the coding sequences as well as in non-translatable regions, i.e., 5’UTR and 3’UTR, of mRNA transcripts. Parallelly, another technique was developed that quantifies specific m6A methylation motifs through a probe-based ELISA process, MAQ-G. This second method successfully validated the N⁶-methyladenosine motifs predicted by the initially developed motif-finder program. This integrated m6A-FINDiT and MAQ-G, coupled with a real-time qPCR assay, could correlate the methylation profiles of N6-methyladenosine motifs with the expression and stability contours of a gene. To establish the physiological implications of these techniques, we chose three tumour-suppressor genes, viz., IRF8, RB1, and TP53 mRNA transcripts, which may undergo m6A methylation at certain DRACH motifs. The m6A-FINDiT pipeline could successfully predict the specific m6A motifs, and the MAQ-G confirmed the methylation profile of the latter. These duo techniques hold potential for use in clinical settings for early cancer detection.