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

Abstract

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.

Plant RNA Binding Proteins as Critical Modulators in Drought, High Salinity, Heat, and Cold Stress Responses: An Updated Overview

“…Consistent with previous results, MhYTP1 overexpression in apples promoted drought tolerance through elevated ABA content, increased stomatal density, reduced stomatal aperture, enhanced the net photosynthesis rate, increased biomass, and increased water use efficiency (WUE) under drought conditions [41]. The cis-regulatory elements of YTH domains and abiotic stress gene expression analyses revealed that YTH proteins might participate in heat, drought, salinity, and cold stresses [18,[38][39][40][41][42]. One of the isoforms of the polyadenylation factor was designated as CPSF30-L, which has YTH domain, and was shown to influence the expression of multiple abiotic stress genes in Arabidopsis [110].…”

m6A‐mediated regulation of crop development and stress responses

“…Accordingly, the m 6 A-mediated stress responses have been extensively studied in ª 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 20, 1447-1455 various crops, including tobacco (Nicotiana tabacum) (Li et al, 2018), rice (Cheng et al, 2021;Shi et al, 2019b;Tian et al, 2021;Zhang et al, 2021a), wheat (Sun et al, 2020;Zhang et al, 2021b), sweet sorghum (Zheng et al, 2021), tomato (Yang et al, 2021), apple (Guo et al, 2021;Mao et al, 2021), and pakchoi (Liu et al, 2020).…”

“…Mutation of m 6 A writers in Arabidopsis induces significant changes in the expression of genes responsive to abiotic and biotic stresses, as revealed by transcriptome analysis (Anderson et al ., 2018 ; Bodi et al ., 2012 ; Hu et al ., 2021a ). Accordingly, the m 6 A‐mediated stress responses have been extensively studied in various crops, including tobacco ( Nicotiana tabacum ) (Li et al ., 2018 ), rice (Cheng et al ., 2021 ; Shi et al ., 2019b ; Tian et al ., 2021 ; Zhang et al ., 2021a ), wheat (Sun et al ., 2020 ; Zhang et al ., 2021b ), sweet sorghum (Zheng et al ., 2021 ), tomato (Yang et al ., 2021 ), apple (Guo et al ., 2021 ; Mao et al ., 2021 ), and pak‐choi (Liu et al ., 2020 ).…”

Regulatory Role of N6-Methyladenosine (m6A) Modification in Osteoarthritis

“…In addition, it has been proved that YTHDF2 can reduce the stability of its targeted methylated mRNA transcript and control its span, while YTHDF1 can ensure the efficient expression of protein from its shared region. These studies have proved that YTHDF family proteins have potential synergistic effect in regulating gene expression ( Sun et al, 2020 ).…”