Chemical RNA Modifications: The Plant Epitranscriptome

Abstract

RNA post-transcriptional modifications create an additional layer to control mRNA transcription, fate, and expression. Considering that they are nongenetically encoded, can be of reversible nature, and involved in fine-tuning gene expression, the landscape of RNA modifications has been coined the "RNA epigenome" or "epitranscriptome." Our knowledge of the plant epitranscriptome is so far limited to 3′-uridylation and internal m 6 A and m 5 C modifications in Arabidopsis. m 6 A is the most abundant and well-studied modification on mRNAs, and involves the activities of evolutionarily conserved "writer" (methyltransferase), "reader" (RNA binding proteins), and "eraser" (demethylases) proteins. In Arabidopsis, m 6 A is crucial for embryogenesis, post-embryonic growth, development, phase transition, and defense responses. Conversely to animals, our understanding of the roles of m 6 A is limited to the finding that it is an mRNA stabilizing mark. Yet likely to exist, its roles in controlling plant mRNA maturation, trafficking, storage, and translation remain unexplored. The m 5 C mark is much less abundant on the transcriptome and our knowledge in plants is more limited. Nonetheless, it is also an important epitranscriptomic mark involved in plant development and adaptive response. Here, we explore the current information on m 6 A and m 5 C marks and report knowledge on their distribution, features, and molecular, cellular, and physiological roles, therefore, uncovering the fundamental importance in plant development and acclimation of RNA epigenetics. Likely to be widespread in the green lineage and given their crucial roles in eukaryotes, the fostering of data and knowledge of epitranscriptome from cultivated plant species is of the utmost importance.

Long-term methylome changes after experimental seed demethylation and their interaction with recurrent water stress inErodium cicutarium(Geraniaceae)

“…This interaction appears to produce a complex epigenomic instability making unpredictable the consequences of experimental re-methylation and water stress on the genome-wide scale. On one hand, 5-Aza application in seeds triggers widespread changes in DNA methylation in adult leaves, but importantly it likely alters the expression of transcriptional and post-transcriptional regulatory proteins as suggested by the DMRs overlapping the orthologous of Methyltransferase 13, RNA-dependent DNA polymerase and 60S ribosomal protein (Litholdo & Bousquet-Antonelli, 2019; Sáez-Vásquez & Delseny, 2019). Interestingly, 5-Aza promoted the hypermethylation of the Ec-S10188_3 gene, which contained 28 differentially methylated cytosines in the promoter region (Table 2) and encodes a putative disease resistance protein, with high identity to Resistance genes analogs 3 (RGA3) in Theobroma cacao (Sekhwal et al ., 2015).…”

Transcriptomic Reprogramming, Alternative Splicing and RNA Methylation in Potato (Solanum tuberosum L.) Plants in Response to Potato Virus Y Infection

“…RNA modifications are an important regulator of numerous cell processes [ 73 , 74 ]. Among the diverse modifications found for mRNAs, N6-methyladenosine (m 6 A) is the most prevalent modification in both plants and animals [ 75 ].…”