Deciphering the epitranscriptome: A green perspective

Abstract

The advent of high-throughput sequencing technologies coupled with new detection methods of RNA modifications has enabled investigation of a new layer of gene regulation - the epitranscriptome. With over 100 known RNA modifications, understanding the repertoire of RNA modifications is a huge undertaking. This review summarizes what is known about RNA modifications with an emphasis on discoveries in plants. RNA ribose modifications, base methylations and pseudouridylation are required for normal development in Arabidopsis, as mutations in the enzymes modifying them have diverse effects on plant development and stress responses. These modifications can regulate RNA structure, turnover and translation. Transfer RNA and ribosomal RNA modifications have been mapped extensively and their functions investigated in many organisms, including plants. Recent work exploring the locations, functions and targeting of N⁶ -methyladenosine (m⁶ A), 5-methylcytosine (m⁵ C), pseudouridine (Ψ), and additional modifications in mRNAs and ncRNAs are highlighted, as well as those previously known on tRNAs and rRNAs. Many questions remain as to the exact mechanisms of targeting and functions of specific modified sites and whether these modifications have distinct functions in the different classes of RNAs.

Keywords: Arabidopsis; N6-methyladenosine (m6A); Pseudouridine (Ψ); RNA 5-methylcytosine (m5C); RNA modifications; epitranscriptome.

Figure 1

RNA modifications in messenger RNAs have distinct deposition patterns Shown is a pictorial representation of relative abundance of the RNA modifications m⁶A, m⁵C and Ψ along mRNA transcripts. These representations are based on transcriptome‐wide RNA bisulfite sequencing data for m⁵C and antibody data for m⁶A in animals and plants. The Ψ abundance is based on a combination of Ψ‐seq and antibody enrichment data from animals. m⁶A is lowly abundant along coding sequences and enriched at long last exons and at the start of 3′UTR's. While the majority of m⁵C sites are detected in the coding sequence of mRNA transcripts, m⁵C sites are statistically enriched in 3′UTR's. For Ψ, the modified sites are evenly distributed along the coding sequence, but are statistically underrepresented in 5′ UTRs.

Figure 2

Distinct catalytic and targeting mechanisms of different RNA modifications in Arabidopsis (A) The predicted Arabidopsis m⁶A ‘writer’ complex is composed of a heterodimer of MTA and MTB, bound to AtFIP37 and potentially other, uncharacterized proteins. In mammals, miRNAs are able to guide the m⁶A ‘writer’ complex, however, it is not known if this targeting mechanism is conserved in plants. Potential m⁶A ‘erasers’ and ‘readers’ have been predicted in Arabidopsis and await further characterization. (B) A model for targeting of m⁵C methylation by TRM4B, based on RNA structure and potentially the presence of other RNA modifications. (C) Proposed H/ACA snoRNP Ψ ‘writer’ complex in Arabidopsis contains a guide H/ACA box snoRNA and the proteins GAR1 (At3g03920/At5g18180) or NAF1 (At1g03530), NHP2 (At5g08180), NOP10 (At2g20490) and the Ψ synthase AtCBF5 (At3g57150).

Figure 3

Potential functions of RNA modifications in mediating interactions between nucleic acids and nucleic acids and proteins RNA modifications have diverse chemical properties and can have different effects on RNA interactions. A spikey, pink ball is used to represent a generic RNA modification. RNA modifications can regulate protein binding to RNA through remodeling of local RNA structure (e.g. ‘m⁶A switches’), increasing or inhibiting protein binding. In addition, RNA modifications could potentially affect other types of interactions, such as R‐loops, which are RNA‐DNA hybrids.