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RNA Methylation Contributes to mRNA Mobility and Root Growth in Plants

RNA methylation in plants

August 6, 2019

RNA epigenetics, also known as epitranscriptomics, is sometimes referred to as the next frontier in molecular biology. There have been nearly 200 different RNA modifications reported, and the biological functions of many of them are currently unknown.

RNA methylation is one of the most abundant types of RNA modifications, and two main types of RNA methylation, m6A and 5-mC, are among the most studied to date.

The m6A modification has been linked to several different aspects of RNA biology, including RNA processing and RNA stability. A recent report suggested that m6A might also play a role in early embryonic development.

5-mC in RNA is abundant and dynamic, but its function remains unknown. Previous reports suggest that it has distinct tissue-specific patterns and that it might play a role in the regulation of chromatin structure.

RNA mobility in plants, which involves the transport of RNA molecule to different plant tissues, is a phenomenon that has been known to exist for years. However, the mechanism involved in RNA transport, as well as the biological role of this activity, are not fully understood.

A recent paper in the journal Current Biology provides evidence that epitranscriptomics plays a role in RNA mobility, and that RNA transport is a required function for RNA-based signaling.

RNA Methylation Overview

RNA methylation was first reported in the 1950s, it was identified in yeast by paper chromatography and UV spectrophotometry. Investigating RNA methylation is easier today due to the development of better and more specific antibodies and other tools. Over the next several decades after being discovered, interest in RNA epigenetics and epitranscriptomics has continued to increase as a result of the new and improved ways of studying these RNA modifications, making it more efficient to learn about their biological functions.

m6A Methylation in RNA

N6-methyladenosine (also known as m6A) was one of the first forms of RNA methylation discovered and it is one of the most abundant RNA modifications. Reports have demonstrated that there are over 12,000 sites of m6A methylation in RNA in the human transcriptome, including m6A methylation in more than 7,000 different protein-coding genes.

The m6A modification appears to most commonly be associated with stop codon-3’ UTR junctions and intron-exon junctions, especially at long introns, suggesting that it likely plays a role in RNA processing.

The enzymes known to add the m6A modification to RNA include the RNA methyltransferases METTL3, METTL14, and WTAP. The demethylase enzymes FTO and ALKBH5 have been shown to remove m6A from RNA. The YTH domain family (YTHDF) proteins, such as YTHDF2, bind to m6A and are thought to guide other proteins there to carry out their functions.

5-mC Methylation in RNA

5-methylcytidine (5-mC) was another one of the first types of RNA methylation variants discovered. It was identified to be present in mammalian mRNAs in the 1970s. While 5-mC is best known for being the most common form of DNA methylation, its role in RNA biology is also becoming increasingly investigated.

There have been reports of human RNAs containing the 5-mC at as many as 10,000 different sites, but there have also been conflicting reports that suggest the number of sites is much fewer, closer to 1,000.

The primary 5-mC RNA methyltransferases that have been identified are DNMT2 (which also methylates DNA) and NSUN2. The ten-eleven translocation (Tet) family of proteins, which are the main enzymes that demethylate 5-mC in DNA, mediate 5-mC demethylation in RNA. The protein Aly/REF associates with 5-mC in RNA and therefore appears to “read” this epigenetic modification.

The function of 5-mC methylation in RNA is not completely understood, but mutations in the gene encoding the 5-mC methyltransferase NSUN2 have been observed to exhibit developmental and neurological phenotypes. 5-mC has also been reported to play a role in the export of RNA from the nucleus, and this is thought to be mediated by its association with Aly/REF.

Mobile RNAs in Plants

Intercellular communication mediated by transporting different proteins and RNA molecules to distant locations is a normal biological mechanism in certain plant species such as Arabidopsis, wine grapes, cucumbers, and watermelons. Thousands of different mRNAs have been shown to be transported across graft junctions to specific regions in plants as a way to respond to the environment and react to stressful conditions.

Although this phenomenon of mobile RNAs has been known to exist for years, the molecular details that control its regulation remain largely unknown.

A previous study observed a correlation between the 5-mC methylation in some noncoding RNAs, such as tRNAs. In that report, tRNAs that were highly mobile tended to be more methylated with 5-mC and the non-mobile tRNAs had low or undetectable levels of 5-mC.

A recent study from an international team of researchers based in Germany, France, and China attempted to extend those studies by investigating the role of 5-mC methylation in mRNA transport in plants.

Link Between RNA Epigenetics, Moving RNAs in Plants, and Root Growth

The team of researchers performed a methylated RNA immunoprecipitation (MeRIP) assay with an antibody specific for 5-mC in RNA and they found that many (>500) different mRNAs contained the 5-mC modification.

Most of the modified RNAs (362 of them) were previously determined to be mobile, leading the scientists to hypothesize that there was a link between 5-mC in RNA and RNA mobility.

Two mRNAs with 5-mC modifications were investigated in more detail, TCTP1 and HSC70.1. They observed that both the TCTP1 and HSC70.1 transcripts were not transported across graft junctions in mutant Arabidopsis plants that did not express the RNA methyltransferase enzymes DNMT2 and NSUN2.

Furthermore, they found that the mobility of the TCTP1 mRNA was important for root development and growth, suggesting that the mobility activity of the transcript plays a key role in its function.

Summary: RNA Methylation Helps RNA Transportation in Plants

The main findings of the paper were that many mobile mRNAs contain the 5-mC modification and that functional RNA methylation activity is required for the mobility of at least some transcripts.

However, there is still a lot left to learn about the relationship between RNA methylation and RNA transport in plants. For example, we don’t yet know what factors are recognizing the 5-mC in RNA and mediating the transport.

It also seems likely that different RNAs will have different requirements for mobility to different parts of the plant. This type of mechanism would allow greater control over the responses to multiple kinds of stimuli.

RNA modification and epitranscriptomics is a rapidly expanding field of science and the continued development of more products, assays, and services to enable the more efficient study of RNA epigenetics will help accelerate the research. We can’t wait to see what comes next!

Reference: Yang, L. et al. m5C Methylation Guides Systemic Transport of Messenger RNA over Graft Junctions in Plants. Current Biology 29: 2465-2476. (2019)

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