Analysis approaches for the identification and prediction of N ⁶ -methyladenosine sites

Abstract

The global dynamics in a variety of biological processes can be revealed by mapping transcriptional m 6 A sites, in particular full-transcriptome m 6 A. And individual m 6 A sites have contributed to biological function, which can be evaluated by stoichiometric information obtained from the single nucleotide resolution. Currently, the identification of m 6 A sites is mainly carried out by experiment and prediction methods, based on high-throughput sequencing and machine learning model respectively. This review summarizes the recent topics and progress made in bioinformatics methods of deciphering the m 6 A methylation, including the experimental detection of m 6 A methylation sites, techniques of data analysis, the way of predicting m 6 A methylation sites, m 6 A methylation databases, and detection of m 6 A modification in circRNA. At the end, the essay makes a brief discussion for the development perspective in this area.

Reduced DNMT1 levels induce cell apoptosis via upregulation of METTL3 in cardiac hypertrophy

“…N6-methyladenosine (m6A) methylation is defined as the adjunction of methyl to adenosine (A) in RNA transcripts [ 18 ]. The m6A process is reversible, and the main recognition site for most RNA methylases is RRACH [ 19 , 20 ]. The dynamic m6A RNA modification is maintained by m6a writers—adenosine methyltransferases, which consist of WTAP, METTL14, METTL3, METTL16 and; m6a erasers—demethylases, which include ALKBH5 and FTO; and m6a readers—binding proteins comprising HNRNPC, HNRNPA2B1, YTHDF2, YTHDF1, and eIF3 [ 21 , 22 ].…”

One-Base-Gap Circular Probe-Mediated Dual Amplification for Isothermal Detection of N6-Methyladenosine Modifications

“…However, the MeRIP-seq or m 6 A-seq techniques offered a limited base resolution of ∼200 bases. Then, researchers introduced a photosensitive cross-linking strategy into antibody immunoprecipitation, substantially enhancing base recognition resolution to ∼30 bases and even a single base. − Although the base resolution had been largely improved, antibody-dependent techniques still suffer from problems such as poor reproducibility, false-positive results, large sample demand, affinity variation of antibodies, and low efficiency, , making it difficult to accurately quantify m 6 A . Liu et al introduced a RNase H cleavage-based method, enabling precise quantification of m 6 A at specific sites using radiolabeling and thin layer chromatography (SCARLET) .…”