Xeno nucleic acid probes mediated methylation-specific PCR for single-base resolution analysis of N6-methyladenosine in RNAs

Reliable and cost-effective quantification of RNA modifications at a specific gene locus is essential to elucidate the pathogenic mechanism encoded by RNA epigenetics. Current methods to quantify N⁶-methyladenosine (m6A) at specific sites can hardly satisfy the requirement of clinical application because epigenetic information is easily lost through polymerase chain reaction (PCR) assay or other isothermal amplification methods unless tedious pretreatment is applied. Herein, we propose a simple xeno nucleic acid (XNA) as a blocker probe to mediate the methylation specific reverse transcription quantitative polymerase chain reaction (MsRT-qPCR) assay to directly magnify the minor differences between epigenetic bases and unmodified bases in RNA. Strand displacement reactions selectively initiated between the reverse transcription primer (RT-primer) and the XNA probe at the m6A template given the affinity differences between the blocker probes and the m6A-modified RNA (m6A-RNA) and unmodified RNA (A-RNA). Thus, preferential amplification of m6A-RNA was allowed. Integration of a well-established oligo-modified Fe₃O₄@UiO-66-NH₄ allowed purification of mRNA and lncRNA from cellular total RNA samples and greatly reduced the non-specific interference of m6A detection in real samples. Multiple specific sites of m6A in mRNA and lncRNA samples are also successfully quantified. The XNA probe-based m6A assay required only common and available lab equipment and materials, which can be applied in m6A-related fundamental studies and clinical diagnosis.

Detection methods of epitranscriptomic mark N6-methyladenosine

Research on N6-methyladenosine (m6A) in recent years has revealed the complex but elegant regulatory role of this RNA modification in multiple physiological processes. The advent of m6A detection technologies is the basis for studying the function of this RNA modification. These technologies enable the detection of m6A sites across transcriptome or at specific gene, thereby revealing the alternation and dynamic of RNA modification. However, non-specific signals that arise from the antibody-based methods and the low-resolution landscape have become the major drawback of classic m6A detection methods. In this review, we summarize the current available methods and categorized them into three groups according to the utilization purpose, including measurement of total m6A levels, detection m6A locus in single gene, and m6A sequencing. We hope this review helps researchers in epitranscriptomic field find an appropriate m6A detection tool that suites their experimental design.