Abstract
BackgroundN6-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.ResultsA 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 N1 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.ConclusionsIn 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.
Highlights
N6-Methyladenosine (m6A) is the most widespread RNA modification that plays roles in the regulation of genes and genome stability
The conserved YT521-B homology (YTH) domain was used to BLASTp the YTH proteins encoded by the wheat genome on the website http://plants.ensembl.org/ Multi/Tools/Blast [8]
An unrooted phylogenetic tree of 39 TaYTH genes was constructed based on the YTH domains of the 39 TaYTHs in concert with 82 YTH proteins from A. thaliana, O. sativa, G. max, Z. mays, B. distachyon, and H. vulgare (Additional file 2) to analyze the evolutionary relationships of the TaYTH proteins (Fig. 1a)
Summary
N6-Methyladenosine (m6A) is the most widespread RNA modification that plays roles in the regulation of genes and genome stability. Many m6A reader proteins have been identified, and most contain a YT521-B homologous (YTH) domain with an aromatic cage that recognizes the GG(m6A) C sequence [7]. In A. thaliana, M. hupehensis and C. sativus, YTH genes are involved in plant responses to pathogens, plant hormones (salicylic acid and abscisic acid), and abiotic stresses (water, temperature, and salinity) [10,11,12,13, 20,21,22] These studies revealed that YTH domain-containing proteins play important roles in plant development and biotic and abiotic stress responses. We identified 39 genes that encode YTH domain-containing proteins in common wheat and analyzed their phylogenetic relationship and expression in different tissues/organs and in response to various stresses
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