Uncovering the Epitranscriptome: A Review on mRNA Modifications and Emerging Frontiers

Background/Objectives: Messenger RNA (mRNA) modifications regulate key steps in gene expression, including splicing, translation, and stability. Despite over 170 known RNA modifications, the subset occurring in mRNA remains understudied compared to tRNA and rRNA. This review aims to systematically evaluate 14 known naturally occurring mRNA-specific modifica-tions, rank them by publication frequency, and highlight emerging frontiers in epi-transcriptomics, including discovering new naturally occurring mRNA modifications, environmental RNA (eRNA) epitranscriptomics, and mirror-RNA generation and de-tection. Methods: We conducted a structured literature review of PubMed-indexed publications to rank mRNA modifications by citation prevalence. Key modifications such as m⁶A, m⁵C, Ψ, and m¹A were analyzed in terms of enzymatic machinery (“writers,” “erasers,” and “read-ers”), molecular functions, and physiological relevance. We also reviewed technological advances, with a focus on nanopore sequencing for detection of RNA modifications in native and environmental contexts. Results: m⁶A was identified as the most studied mRNA modification, followed by Ψ, m⁵C, and A-to-I editing (inosine). These modifications influence diverse mRNA processes, in-cluding translation efficiency, localization, and immune evasion. Cap-specific modifica-tions such as Cap0, Cap1, and Cap2 were also described, highlighting their role in transcript stability and innate immune regulation. Advances in nanopore sequencing have enabled direct detection of RNA modifications and offer promise for eRNA (envi-ronmental RNA) surveys. The potential for nanopore sequencing of many other of the 335 known RNA modifications in the MODOMICS database using existing nanopore tech-nologies and mirror-RNAs and mirror RNA modifications using mirror helicases is also discussed. Conclusions: mRNA modifications represent a critical, yet incompletely mapped, layer of gene reg-ulation. Continued research—especially using nanopore and machine learning tech-nologies—will help uncover their full biological significance. Exploration of eRNA and mirror-RNA modification space may redefine our understanding of RNA biology and origins of life.