Abstract
Circadian regulations are essential for enabling organisms to synchronize physiology with environmental light-dark cycles. Post-transcriptional RNA modifications still represent an understudied level of gene expression regulation in plants, although they could play crucial roles in environmental adaptation. N6-methyl-adenosine (m6A) is the most prevalent mRNA modification, established by “writer” and “eraser” proteins. It influences the clockwork in several taxa, but only few studies have been conducted in plants and none in marine plants. Here, we provided a first inventory of m6A-related genes in seagrasses and investigated daily changes in the global RNA methylation and transcript levels of writers and erasers in Cymodocea nodosa and Zostera marina. Both species showed methylation peaks during the dark period under the same photoperiod, despite exhibiting asynchronous changes in the m6A profile and related gene expression during a 24-h cycle. At contrasting latitudes, Z. marina populations displayed overlapping daily patterns of the m6A level and related gene expression. The observed rhythms are characteristic for each species and similar in populations of the same species with different photoperiods, suggesting the existence of an endogenous circadian control. Globally, our results indicate that m6A RNA methylation could widely contribute to circadian regulation in seagrasses, potentially affecting the photo-biological behaviour of these plants.
Highlights
Epigenetic modifications include all changes that provide heritable phenotypes while not altering the DNA sequence itself, such as chemical modifications of DNA and its associated proteins, or changes caused by small RNA molecules [1]
In the Z. marina genome, single proteins represented MTA, MTB, and HAKAI, while FIP37 resulted in a gene family of six members (Table 1, Figures 1 and 2)
Seagrasses possess the entire repertoire of m6A writers and eraser genes (i.e., MTA/B, FIP37, HAKAI, VIRILIZER, and ALKBH9B/10B); an expansion of the FIP37 gene family was observed at the gene and transcript levels
Summary
Epigenetic modifications include all changes that provide heritable phenotypes while not altering the DNA sequence itself, such as chemical modifications of DNA (e.g., methylation) and its associated proteins (e.g., histone modifications), or changes caused by small RNA molecules (e.g., gene silencing by noncoding RNAs) [1]. These multiple epigenetic mechanisms are critical for regulating the chromatin condensation state and directly affect gene expression during organismal development and in response to environmental stressors [2,3,4]. In plants m6A sites are enriched around the stop codon and within 3 untranslated regions (3 UTRs), and around the start codon of CDS [20,21], indicating that m6A modifications can regulate all stages of mRNA life
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