Genome-Wide Identification and Expression Analysis of the YTH Domain-Containing RNA-Binding Protein Family in Cinnamomum camphora

Abstract

N6-methyladenosine (m6A) is one of the most abundant chemical modifications on mRNA in eukaryotes. RNA-binding proteins containing the YT521-B (YTH) domain play crucial roles in post-transcriptional regulation of plant growth, development, and stress response by reading the m6A mark. However, the YTH domain-containing RNA-binding protein family has not been studied in a valuable and medicinal tree such as Cinnamomum camphora (C. camphora) yet. In this study, we identified 10 YTH genes in C. camphora, located on eight out of 12 chromosomes. Phylogenetic analysis revealed that these genes can be classified into two major classes, YTHDF (CcDF) and YTHDC (CcDC). Closely related CcYTHs within the same class exhibited a similar distribution of conserved motifs and domain organization, suggesting functional similarities among these closely related CcYTHs. All CcYTH proteins possessed a highly conserved YTH domain, with CcDC1A containing an additional CCCH domain. The liquid–liquid phase separation (LLPS) predictions indicate that CcDC1A, CcDF1A, CcDF1C, CcDF3C, CcDF4C, and CcDF5C may undergo phase transitions. Quantitative expression analysis revealed that tissue-specific expression was observed fo CcYTHs. Notably, there were two genes, CcDF1A and CcDF5C; both exhibited significantly higher expression levels in various tissues than other genes, indicating that the m6A-YTH regulatory network in C. camphora might be quite distinct from that in most plants such as Arabidopsis thaliana (A. thaliana) with only one abundant YTH protein. According to the analysis of the up-stream cis-regulatory elements of these YTH genes, these genes could be closely related to stress, hormones, and development. The following stress response experiments further verified that their expression levels indeed changed under both PEG and NaCl treatments. These findings not only provide a foundation for future functional analysis of CcYTHs in C. camphora, but also provide insights into the functions of epigenetic mark m6A in forest trees.

Detection, distribution, and functions of RNA N6-methyladenosine (m6A) in plant development and environmental signal responses

“…m 6 A modification influences seed germination, root growth, floral morphogenesis, plant height, fruit ripening, and senescence during plant growth and development ( Lu et al., 2020 ; Tang et al., 2021 ; Rudy et al., 2022 ; Xu et al., 2022 ; Hu et al., 2022a ; Xu et al., 2023 ; Cai et al., 2023b a; Sheikh et al., 2024 ). In addition, it plays a role in the responses of plants to abiotic environmental signals such as drought, cold, and heavy metal stress ( Lu et al., 2020 ; Cheng et al., 2021 ; Vicente et al, 2023 ; Zhang et al, 2024 ). Furthermore, during plant viral infection, m 6 A modification may exhibit positive or negative functions ( Cheng et al., 2021 ; Martínez-Pérez et al., 2023 ; Wang et al., 2023b ; Yao et al, 2023b ).…”