Single-nucleotide resolution of N 6-adenine methylation sites in DNA and RNA by nitrite sequencing.

Yasaman Mahdavi-Amiri,Kimberley Chung Kim Chung,Ryan Hili

doi:10.1039/d0sc03509b

Abstract

A single-nucleotide resolution sequencing method of N6-adenine methylation sites in DNA and RNA is described. Using sodium nitrite under acidic conditions, chemoselective deamination of unmethylated adenines readily occurs, without competing deamination of N6-adenine sites. The deamination of adenines results in the formation of hypoxanthine bases, which are read by polymerases and reverse transcriptases as guanine; the methylated adenine sites resist deamination and are read as adenine. The approach, when coupled with high-throughput DNA sequencing and mutational analysis, enables the identification of N6-adenine sites in RNA and DNA within various sequence contexts.

Highlights

The ability to map methylation sites in the human genome and epitranscriptome has transformed our understanding of how these modi cations govern and in uence a host of cellular processes and diseases.[1,2] Amongst the most widely studied methylations is N6-methyladenine, known as 6mA in DNA and m6A in RNA. m6A is the most common methylation observed in RNA, where it constitutes 0.1–0.4% of adenosines, and accounts for approximately 50% of total methylations in RNA.[3]
The dynamics of m6A incorporation into RNA are regulated by “writers” and “erasers”, and can directly affect processes such as nuclear RNA export, splicing, and RNA stability.[4]. The deregulation of these dynamics and resulting aberrant levels of m6A has been linked to obesity, immunoregulation, and cancer.[5]
While 6mA has been widely known as a DNA modi cation in prokaryotes, its presence in eukaryotes has only been recently established, including in humans where it represents $0.051% of the genome.6 6mA is thought to play an epigenetic role in embryonic development,[7] tumorigenesis,[6] response to stress, neuropsychiatric disorders,[8] and embryonic stem cell function,[9] and it can be inherited.[10]

Summary

Introduction

The ability to map methylation sites in the human genome and epitranscriptome has transformed our understanding of how these modi cations govern and in uence a host of cellular processes and diseases.[1,2] Amongst the most widely studied methylations is N6-methyladenine, known as 6mA in DNA and m6A in RNA. m6A is the most common methylation observed in RNA, where it constitutes 0.1–0.4% of adenosines, and accounts for approximately 50% of total methylations in RNA.[3]. Single-nucleotide resolution of N6-adenine methylation sites in DNA and RNA by nitrite A single-nucleotide resolution sequencing method of N6-adenine methylation sites in DNA and RNA is described.

Results

Conclusion