The RNA modification landscape in human disease

Abstract

RNA modifications have been historically considered as fine-tuning chemo-structural features of infrastructural RNAs, such as rRNAs, tRNAs, and snoRNAs. This view has changed dramatically in recent years, to a large extent as a result of systematic efforts to map and quantify various RNA modifications in a transcriptome-wide manner, revealing that RNA modifications are reversible, dynamically regulated, far more widespread than originally thought, and involved in major biological processes, including cell differentiation, sex determination, and stress responses. Here we summarize the state of knowledge and provide a catalog of RNA modifications and their links to neurological disorders, cancers, and other diseases. With the advent of direct RNA-sequencing technologies, we expect that this catalog will help prioritize those RNA modifications for transcriptome-wide maps.

Keywords: RNA modification; detection methods; direct RNA sequencing; disease; epitranscriptome.

FIGURE 1.

RNA modifications and their links to human disease. The set of known RNA modifications classified by their reference nucleotide, highlighting those that have been associated to human diseases (red), as well as those for which a transcriptome-wide detection method has been established (circled in green).

FIGURE 2.

Current genome-wide detection methods used to identify RNA modifications. (A) In the left panel, antibody-based methods (RIP-seq) show how RNA-modification enriched fragments are selected using pool-down, and compared to a total fragmented sample (input), which is used for normalization, obtaining genome-wide maps with peak resolution. (B) In the middle panel, RNA samples are pretreated with chemical reagents (Chem-seq), which inhibit the reverse transcription reaction beyond the chemically modified position. (C) In the right panel, mismatch signature-based methods, which are based on the increased mismatch rates that occur upon reverse transcription at certain RNA-modified positions, are depicted.

FIGURE 3.

Direct RNA sequencing library preparation steps using Oxford Nanopore Technologies. (A) Schematic representation of a nanopore embedded in the membrane of the flowcell. (B) Overview of the main library preparation steps in ONT direct RNA sequencing.