N6‐methyladenosine regulatory machinery in plants: composition, function and evolution

Yue, Hong; Nie, Xiaojun; Yan, Zhaogui

doi:10.1111/pbi.13149

Cited by 145 publications

(147 citation statements)

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“…In our study, a total of 39 putative YTH domain-containing protein family genes were identified in common wheat. Yue et al identified 41 m6A reader proteins in wheat [25], and 38 of them contained the YTH domain. We identified an additional wheat gene, TaDC1a-7D (TraesCS7D02G450100.1), which encodes a protein containing YTH domain at its middle part, and was designated member of the wheat YTHDC group (Table 1).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

et al. 2020

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Background: N6-Methyladenosine (m6A) is the most widespread RNA modification that plays roles in the regulation of genes and genome stability. YT521-B homology (YTH) domain-containing RNA-binding proteins are important RNA binding proteins that affect the fate of m6A-containing RNA by binding m6A. Little is known about the YTH genes in common wheat (Triticum aestivum L.), one of the most important crops for humans. Results: A total of 39 TaYTH genes were identified in common wheat, which are comprised of 13 homologous triads, and could be mapped in 18 out of the 21 chromosomes. A phylogenetic analysis revealed that the TaYTHs could be divided into two groups: YTHDF (TaDF) and YTHDC (TaDC). The TaYTHs in the same group share similar motif distributions and domain organizations, which indicates functional similarity between the closely related TaYTHs. The TaDF proteins share only one domain, which is the YTH domain. In contrast, the TaDCs possess three C3H1-type zinc finger repeats at their N-termini in addition to their central YTH domain. In TaDFs, the predicated aromatic cage pocket that binds the methylysine residue of m6A is composed of tryptophan, tryptophan, and tryptophan (WWW). In contrast, the aromatic cage pocket in the TaDCs is composed of tryptophan, tryptophan, and tyrosine (WWY). In addition to the general aspartic acid or asparagine residue used to form a hydrogen bond with N 1 of m6A, histidine might be utilized in some TaDFb proteins. An analysis of the expression using both online RNA-Seq data and quantitative real-time PCR verification revealed that the TaDFa and TaDFb genes are highly expressed in various tissues/organs compared with that of TaDFcs and TaDCs. In addition, the expression of the TaYTH genes is changed in response to various abiotic stresses. Conclusions: In this study, we identified 39 TaYTH genes from common wheat. The phylogenetic structure, chromosome distribution, and patterns of expression of these genes and their protein structures were analyzed. Our results provide a foundation for the functional analysis of TaYTHs in the future.

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Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

et al. 2020

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“…m 6 A is not expected to rewire the genetic code for translation (Dai et al , ). m 6 A‐RNA modifications seem to serve important regulatory roles in gene expression in animals and plants, as well in various prokaryotic organism (see for example Batista, ; Meyer and Jaffrey, ; Arribas‐Hernández et al , ; Visvanathan and Somasundaram, ; and Yue et al , , and references therein).…”

Section: Discussionmentioning

confidence: 99%

Topologies of N⁶‐adenosine methylation (m⁶A) in land plant mitochondria and their putative effects on organellar gene expression

et al. 2019

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Summary Mitochondria serve as major sites of ATP production and play key roles in many other metabolic processes that are critical to the cell. As relicts of an ancient bacterial endosymbiont, mitochondria contain their own hereditary material (i.e. mtDNA, or mitogenome) and a machinery for protein biosynthesis. The expression of the mtDNA in plants is complex, particularly at the post‐transcriptional level. Following transcription, the polycistronic pre‐RNAs undergo extensive modifications, including trimming, splicing and editing, before being translated by organellar ribosomes. Our study focuses on N6‐methylation of adenosine ribonucleotides (m6A‐RNA) in plant mitochondria. m6A is a prevalent modification in nuclear‐encoded mRNAs. The biological significance of this dynamic modification is under investigation, but it is widely accepted that m6A mediates structural switches that affect RNA stability and/or activity. Using m6A‐pulldown/RNA‐seq (m6A‐RIP‐seq) assays of Arabidopsis and cauliflower mitochondria, we provide information on the m6A‐RNA landscapes in Arabidopsis thaliana and Brassica oleracea mitochondria. The results show that m6A targets different types of mitochondrial transcripts, including known genes, mtORFs, as well as non‐coding (transcribed intergenic) RNA species. While ncRNAs undergo multiple m6A modifications, N6‐methylation of adenosine residues with mRNAs seem preferably positioned near start codons and may modulate their translatability.

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“…More than 100 types of chemical modifications have been discovered in cellular RNAs . Reversible RNA modifications are an emerging layer of posttranscriptional gene regulation, which exerts a large number of physiological processes and biological functions . As a novel epitranscriptomic marker, the dynamic and reversible chemical N 6 ‐methyladenine (m 6 A) modification is the most abundant internal modification in mRNA.…”

Section: Introductionmentioning

confidence: 99%

Emerging role of m⁶A RNA methylation in nutritional physiology and metabolism

Frazier

Zhang

et al. 2019

Obesity Reviews

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N 6 -methyladenine (m 6 A) is the most prevalent type of internal RNA methylation in eukaryotic mRNA and plays critical roles in regulating gene expression for fundamental cellular processes and diverse physiological functions. Recent evidence indicates that m 6 A methylation regulates physiology and metabolism, and m 6 A has been increasingly implicated in a variety of human diseases, including obesity, diabetes, metabolic syndrome and cancer. Conversely, nutrition and diet can modulate or reverse m 6 A methylation patterns on gene expression. In this review, we summarize the recent progress in the study of the m 6 A methylation mechanisms and highlight the crosstalk between m 6 A modification, nutritional physiology and metabolism. KEYWORDS epitranscriptomic, M 6 A RNA methylation, metabolism, nutrition 1 | INTRODUCTION More than 100 types of chemical modifications have been discovered in cellular RNAs. 1 Reversible RNA modifications are an emerging layer of posttranscriptional gene regulation, 2,3 which exerts a large number of physiological processes and biological functions. 4,5 As a novel epitranscriptomic marker, the dynamic and reversible chemical N 6methyladenine (m 6 A) modification is the most abundant internal modification in mRNA. In mammals, plants and some prokaryotes, m 6 A is widely involved in mRNA metabolism, including mRNA stability, 6 mRNA splicing, 7,8 RNA nucleation, 9 RNA-protein interactions 10 and mRNA translation. 11The m 6 A modification plays an important role in nutritional physiology and metabolism, such as controlling circadian rhythms, 12,13 lipid accumulation 14 and adipogenesis. 15,16 The dysregulation of m 6 A patterns causes abnormal gene expression and functions, aberrant cell differentiation and cellular homeostasis imbalance, leading to the occurrence of certain inflammatory states, metabolic diseases and cancer. 9,17,18 Therefore, the effects of m 6 A RNA methylation on physiology and metabolism have become a research hotspot in the RNA Abbreviations: m 6 A, N 6 -methyladenine; 3'-UTRs, 3'untranslated regions; CDS, coding sequence; MTC, methyltransferase cpmplex; METTL3, methyltransferase-like 3; METTL14, methyltransferase-like 14; WTAP, Wilms' tumour 1-associating protein; ZC3H13, zinc finger CCCH-type containing 13; RBM15/15B, RNA binding motif protein 15/15B; FTO, fat mass and obesity-associated protein; ALKBH5, AlkB homolog 5; YTHDF1/2/3, YTH domain family 1/2/3; YTHDC1/2, YTH domain containing 1/2; SAM, S-adenosylmethionine; hm 6 A, N 6hydroxymethyladenosine; f 6 A, N 6 -formyladenosine; A, adenosine; m 6 A m , N 6 ,2'-O-dimethyladenosine; DCP2, decapping mRNA 2; snRNA, small nuclear RNA; eIF3, eukaryotic initiation factor 3; SRSF3, serine/arginine-rich splicing factor 3; SRSF10, serine/arginine-rich splicing factor 10; HNRNPA2B1, heterogenous nuclear ribonucleoprotein A2B1; HNRNPC, heterogenous nuclear ribonucleoprotein C; DGCR8, DiGeorge syndrome critical region gene 8; IGF2BP1/2/3, insulin-like growth factor 2 mRNA-binding protein 1/2/3; T2DM, type 2 diabetes melli...

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N6‐methyladenosine regulatory machinery in plants: composition, function and evolution

Cited by 145 publications

References 86 publications

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

Topologies of N⁶‐adenosine methylation (m⁶A) in land plant mitochondria and their putative effects on organellar gene expression

Emerging role of m⁶A RNA methylation in nutritional physiology and metabolism

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N6‐methyladenosine regulatory machinery in plants: composition, function and evolution

Cited by 145 publications

References 86 publications

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

Topologies of N6‐adenosine methylation (m6A) in land plant mitochondria and their putative effects on organellar gene expression

Emerging role of m6A RNA methylation in nutritional physiology and metabolism

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Topologies of N⁶‐adenosine methylation (m⁶A) in land plant mitochondria and their putative effects on organellar gene expression

Emerging role of m⁶A RNA methylation in nutritional physiology and metabolism