Mapping the epigenetic modifications of DNA and RNA

Abstract

Over 17 and 160 types of chemical modifications have been identified in DNA and RNA, respectively. The interest in understanding the various biological functions of DNA and RNA modifications has lead to the cutting-edged fields of epigenomics and epitranscriptomics. Developing chemical and biological tools to detect specific modifications in the genome or transcriptome has greatly facilitated their study. Here, we review the recent technological advances in this rapidly evolving field. We focus on high-throughput detection methods and biological findings for these modifications, and discuss questions to be addressed as well. We also summarize third-generation sequencing methods, which enable long-read and single-molecule sequencing of DNA and RNA modification.

Keywords: DNA methylation; DNA modification; RNA modification; epigenetics; epitranscriptomics; long read sequencing.

Figure 1

Single-base resolution methods for quantitatively profiling mammalian DNA modifications of cytosine. For 5 methylcytosine (5mC) mapping there are three methods, whole-genome bisulfite sequencing (WGBS), TET-assisted pyridine borane sequencing (TAPS) and enzymatic methyl-sequencing (EM-Seq); For 5-hydroxymethylcytosine (5hmC) mapping in single-base resolution there are four methods, oxidative bisulphite sequencing (oxBS-Seq), TET-assisted bisulphite sequencing (TAB-Seq) and APOBEC-coupled epigenetic sequencing (ACE-Seq) as well as chemical-assistant C-to-T conversion of 5hmC sequencing (hmC-CATCH); Four sequencing methods for mapping the 5-formylcytosine (5fC), chemically assisted bisulfite sequencing (fCAB-Seq), reduced BS-Seq (redBS-Seq), M.SssI methylase-assisted bisulfite sequencing (MAB-Seq) and 5fC cyclization-enabled C-to-T transition of 5fC (fC-CET); Chemical modification-assisted bisulfite sequencing (CAB-Seq) is a singe-base resolution sequencing method to map 5caC

Figure 2

Chemical structures, modification enzymes and high-throughput detection strategies of modifications in the transcriptome