Epigenetic Modifications of mRNA and DNA in Plants

Abstract

Advances in the detection and mapping of messenger RNA (mRNA) N 6 -methyladenosine (m 6 A) and 5-methylcytosine (m 5 C), and DNA N 6 -methyldeoxyadenosine (6mA) redefined our understanding of these modifications as additional tiers of epigenetic regulation. In plants, the most prevalent internal mRNA modifications, m 6 A and m 5 C, play crucial and dynamic roles in many processes, including embryo development, stem cell fate determination, trichome branching, leaf morphogenesis, floral transition, stress responses, fruit ripening, and root development. The newly identified and widespread epigenetic marker 6mA DNA methylation is associated with gene expression, plant development, and stress responses. Here, we review the latest research progress on mRNA and DNA epigenetic modifications, including the detection, dynamics, distribution, functions, regulatory proteins, and evolution, with a focus on m 6 A, m 5 C, and 6mA. We also provide some perspectives on future research of the newly identified and unknown epigenetic modifications of mRNA and DNA in plants.

Gene Signature and Identification of Clinical Trait-Related m6 A Regulators in Pancreatic Cancer

“…Both coding RNAs and some non-coding RNAs, such as lncRNA, microRNA, tRNA, and rRNA and RNA splice body, were regulated by an m 6 A modification before and after transcription (Yen et al, 2019). N6-methyladenosine modification is closely related to the metabolic processes of RNAs, for example, RNA processing, RNA transfer from the nucleus to the cytoplasm, RNA translation, RNA decay, and the biogenesis of RNA (Liang et al, 2020). The dynamic modification of RNA as a way of regulating genetic information is a new field of study, so there is still a lot of work to be done to understand the underlying mechanisms.…”

Mapping the epigenetic modifications of DNA and RNA

“…Not only a cap modification, but also an internal modification: m 7 G m 7 G is a well-known mRNA cap modification. It is also prevalent in tRNA and recently has been identified in mRNA as well (Chu et al, 2018;Malbec et al, 2019;Zhang et al, 2019a). METTL1-WDR4, known as a tRNA m 7 G methyltransferase complex, installs a subset of internal m 7 G in mRNA (Fig.…”

“…m 7 G-MeRIP-Seq used m 7 G-specific antibody to identified over 2,000 internal m 7 G peaks in the mammalian transcriptome (Zhang et al, 2019a). m 7 G miCLIP-Seq utilized cross-linking-induced truncation and mutation to detect m 7 G (Malbec et al, 2019). m 7 G-Seq adopted a reduction-induced depurination reaction to generate a basic site at m 7 G positions, which can be further labeled with biotin and subsequently pulled down.…”

“…The labeled m 7 G sites in RNA can cause misincorporation during RT, thus achieving the base-resolution map of m 7 G methylome (Zhang et al, 2019a). Benefiting from high-throughput detection strategies, two groups independently found that internal m 7 G in mRNA plays regulatory roles in translation (Malbec et al, 2019;Zhang et al, 2019a). Considering that METTL1modified m 7 G in tRNA is also required for translation and modification enzymes are shared between mRNA and tRNA (Lin et al, 2018), it would be interesting to separately probe its function in mRNA.…”

m6A RNA Methylation in Marine Plants: First Insights and Relevance for Biological Rhythms

“…In parallel, the term ‘epitranscriptomics’ comprises all modifications of RNA molecules that do not affect their sequence [ 5 ]. Similar to epigenetic changes involving the genome structure, RNA modifications are emerging as fundamental players in the field of post-transcriptional regulation of gene expression in both plants and animals, and are attracting a comparable interest to that of DNA and histone modifications [ 5 , 6 , 7 , 8 ]. Furthermore, emerging studies are highlighting the roles of RNA methylation as an epigenetic marker for RNA-dependent inheritance [ 9 , 10 ] and the induction of a stable phenotypic variation [ 11 ].…”