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RNA demethylation induces increased crop biomass and productivity in the field

ABSTRACT: We performed the transcriptome-wide m6A profiling (MeRIP) with poly(A) RNA samples isolated from shoots and roots of wild type (Nipp), FTO homogeneous transgenic (FTO) and demethylation activity dead mutant variant of FTO transgenic (FTOmut) rice plants. The m6A motif and the distribution of the detected m6A sites along transcripts were consistent with reported results from previous m6A sequencing studies in plants. We then analyzed the differentially methylated m6A sites in poly(A) RNA species including those transcribed from gene loci and from repetitive elements (repeat RNAs). Compared to Nipp plants, both shoots and roots of FTO transgenic plants had showed more hypomethylated m6A peaks (hypo-m6A, 222 in shoots and 3313 in roots) than hypermethylated m6A peaks (hyper-m6A, 63 in shoots and 127 in roots) in mRNAs, while FTOmut rice had showed more hyper-m6A in shoots (349 for hyper vs 31 for hypo) but more hypo-m6A in roots (291 for hyper vs 380 for hypo) than the WT. The hypomethylated m6A peaks in FTO transgenic plants were highly enriched within 3'UTR. Gene Ontology (GO) analysis of these identified hypomethylated m6A-containing coding genes in both FTO transgenic rice shoots and roots revealed an enrichment for functional annotations related to “cellular homeostatic process”, “one-carbon and small molecule metabolic process”, and “gene expression”. We also found the extent of m6A hypomethylation was more pronounced for repeat RNAs than for mRNA species.The quantitative RNA-seq analysis that included ERCC spike-in controls confirmed that FTO plants do indeed accumulate higher overall levels of poly(A) RNA than do WT shoots and roots. Above all, FTO mediated m6A demethylation in plant mRNA and repeats RNA, leading to the activation of transcription.

ORGANISM(S): Oryza sativa

PROVIDER: GSE135549 | GEO | 2021/08/11

REPOSITORIES: GEO

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Project description:This research aims at assessing the m6A methylome in the RA peripheral blood mononuclear cells (PBMCs) and perform potential drug targets prediction analysis. Five RA samples and ten control samples were obtained from China-Japan Friendship Hospital. The various expression of m6A methylation and genes in RA and control group were compared with methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq). Bioinformatics explorations were also made to explore the enriched biological roles and paths of the differentially expressed m6A methylation and genes. Potential drug targets prediction and validation were also constructed to provide potential therapeutic targets for RA. In total, 583 dysregulated m6A peaks, of which 295 were greatly upregulated and 288 were greatly downregulated, were identified. Similarly, 1570 differentially genes were acquired by RNA-seq, including 539 upregulated and 1031 downregulated. According to deeper joint exploration, the m6A methylation and mRNA expression degrees of 35 genes varied greatly, of which including 13 hyper-methylated as well as upregulated genes (hyper-up), 12 hyper-methylated and downregulated genes (hyper-down), 5 hypo-methylated as well as upregulated genes (hypo-up), and 5 hypo-methylated and downregulated genes (hypo-down) GO and KEGG explorations showed the enrichment of these distinct genes in “protein transport” “protein binding” and “lysosome”. In addition, the mRNA levels of TUBB2A, IGF2BP3, DYNC1I1 and FOSL1 were increased and consistent with the trend of our sequencing results. While after the treatment of TP and MTX, their mRNA levels were decreased. This research set up the transcriptional map of m6A in RA PBMCs and displayed the hidden association between RNA methylation alternation and associated genes in RA. The outcomes highlight the importance of m6A modification as a gene regulatory system in RA. Furthermore, TUBB2A, IGF2BP3, DYNC1I1 and FOSL1 might be potential therapeutic targets of TP and MTX during RA treatment.

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RNA demethylation induces increased crop biomass and productivity in the field

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