Before you start
- You've done RNA structure and CLIP-seq. They set up why modifications and protein binding interact.
- No coding here. The next lesson covers how m6A is actually measured (m6A-seq / MeRIP).
- Any term new? The Glossary has it.
Learning objectives
By the end of this lesson you will be able to: explain what epitranscriptomics adds on top of the RNA sequence, locate m6A by its DRACH motif, describe the writer, eraser, and reader system that controls it, and place m6A within the wider landscape of RNA modifications.
A second layer of information on RNA
Over 170 distinct chemical modifications have been catalogued across cellular RNAs. Together they form the epitranscriptome: information written on top of the RNA sequence, without changing the sequence itself. The concept mirrors epigenetics on DNA, and the consequences are similar. Two identical mRNA molecules with different modification patterns can have completely different fates.
The star of the field is m6A (N6-methyladenosine): a methyl group added to the nitrogen-6 position of adenosine. It is the most abundant internal modification of eukaryotic messenger RNA, and unlike many marks it is dynamic and reversible, which is what makes it a genuine regulatory switch rather than a fixed tag.
Decode the jargonEpitranscriptome
The complete set of chemical modifications on a cell's RNA. "Epi-" means "on top of": the modifications add a regulatory layer above the underlying RNA sequence, analogous to how the epigenome layers marks on top of the DNA sequence.
Where m6A sits: the DRACH motif
m6A is not placed randomly. It occurs within a consensus sequence usually written DRACH, where the bold A is the methylated adenosine and the letters are IUPAC ambiguity codes:
- D = A, G, or U · R = A or G · A = the methylated adenosine · C = C · H = A, C, or U
Transcriptome-wide maps (the founding 2012 studies by Dominissini et al. and Meyer et al.) showed that m6A is strikingly enriched near stop codons and in 3' untranslated regions, with some in long internal exons. That location is a clue to function: it sits exactly where decisions about translation termination, stability, and 3' UTR-based regulation are made.
The writer–eraser–reader system
m6A is controlled by three classes of proteins. This framework is the core mental model of the whole field.
Writers
Add the methyl group. The core is the METTL3–METTL14 complex: METTL3 is the catalytic subunit, METTL14 is a structural partner that helps bind RNA. WTAP and others recruit and localize the complex.
Erasers
Remove the methyl group, making the mark reversible. ALKBH5 is the major mRNA m6A demethylase; FTO acts more on the related cap-adjacent mark m6Am than on internal m6A in cells.
Readers
Recognize the mark and decide the outcome. Different readers pull the RNA toward different fates, so the same m6A means different things depending on who reads it.
The readers are where the biology gets decided. Classic examples: YTHDF2 directs methylated mRNAs toward degradation; YTHDF1 can promote their translation; the nuclear reader YTHDC1 influences splicing and export; and the IGF2BP family acts to stabilize methylated transcripts. So m6A does not have one fixed effect. Its consequence depends on which reader engages it, in which compartment, on which transcript.
⚠️ A common misconception: "FTO is the m6A eraser"
FTO was the first reported m6A demethylase and is still often described that way, but later work showed FTO prefers m6Am (a modification on the first transcribed nucleotide next to the cap) and acts on cap-proximal sites. In cells, ALKBH5 is the principal eraser of internal m6A. Getting this distinction right is a mark of genuine fluency in the field.
Why m6A matters
By tuning stability, translation, splicing, and export, m6A shapes how quickly a cell can change its protein output. It is central to embryonic development and stem-cell differentiation, the stress and heat-shock response, the immune response, the circadian clock, and is dysregulated in many cancers, which has made the writers and erasers active drug targets. m6A is, in short, a fast, reversible control knob on gene expression that operates entirely at the RNA level.
m6A is not alone: the wider modification landscape
m6A gets the spotlight, but several other modifications are biologically important and increasingly mappable:
| Modification | What it is | Note |
|---|---|---|
| Pseudouridine (Ψ) | An isomer of uridine, the "fifth nucleotide." | The most abundant RNA modification overall; affects stability and structure. |
| m5C | 5-methylcytosine on RNA. | Roles in export and stability; mirrors the DNA mark. |
| m1A | 1-methyladenosine. | Can block base pairing; found in tRNA, rRNA, some mRNA. |
| A-to-I editing | ADAR enzymes convert adenosine to inosine. | Inosine is read as guanosine, so it can recode proteins and alter splicing. |
| m6Am, m7G, 2'-O-methyl | Cap-associated and ribose modifications. | Affect stability and translation; m6Am is the FTO target above. |
Check your understanding
Sources & further reading
- Dominissini D, et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature, 2012.
- Meyer KD, et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell, 2012.
- Zaccara S, Ries RJ, Jaffrey SR. Reading, writing and erasing mRNA methylation. Nat Rev Mol Cell Biol, 2019. (Authoritative review of the writer/eraser/reader system.)
- Roundtree IA, et al. Dynamic RNA modifications in gene expression regulation. Cell, 2017.
Last reviewed: June 2026.