Genome-wide Identification and Expression Analysis of Protein Arginine Methyltransferase and JmjC Domain-containing Family in Apple

Overview

Journal Front Plant Sci

Date 2024 Jun 12

PMID 38863543

Authors

Shenghui Su

Min Ji

Jiaqi Chen

Meidie Zhang

Xiaozhao Xu

Chenxia Cheng

Affiliations

Soon will be listed here.

Abstract

Histone methylation is an important type of histone modification that regulates gene expression in plants. In this study, we identified 14 arginine methylation-related genes (, ) and 32 demethylation-related genes (, ) in apple. Furthermore, we investigated the phylogenetic relationship, chromosome distribution, gene structure, motif analysis, promoter sequence analysis, and expression patterns of and genes. Homology analysis showed a high degree of conservation and homology between and genes in and apple. We identified the types of duplicated genes in the and gene families, found a large number of whole-genome duplicates (WGD) gene pairs and a small number of tandem duplicates (TD) pairs, transposed duplication (TRD) gene pairs as well as proximal duplicates (PD) pairs, and discussed the possible evolutionary pathways of the gene families from the perspective of duplicated genes. Homology analysis showed a high degree of conservation and homology between and genes in and apple. In addition, the promoter regions of and contain numerous -acting elements involved in plant growth and development, hormone response, and stress responses. Based on the transcriptional profiles of and in different tissues and developmental stages, it was found that and may play multiple roles in apple growth and development, for example, may be involved in the regulation of apple endosperm formation. and exhibit different expression patterns in response to hormone signaling in apple, , , , , , and may play roles in apple response to drought stress, while the expression of , , , and is affected by cold stress. Our study provides a foundation for determining the functional roles of and genes in apple.

References

Jenuwein T, Allis C . Translating the histone code. Science. 2001; 293(5532):1074-80. DOI: 10.1126/science.1063127. View

Niu L, Zhang Y, Pei Y, Liu C, Cao X . Redundant requirement for a pair of PROTEIN ARGININE METHYLTRANSFERASE4 homologs for the proper regulation of Arabidopsis flowering time. Plant Physiol. 2008; 148(1):490-503. PMC: 2528109. DOI: 10.1104/pp.108.124727. View

Zhao J, Guo R, Guo C, Hou H, Wang X, Gao H . Evolutionary and Expression Analyses of the Apple Basic Leucine Zipper Transcription Factor Family. Front Plant Sci. 2016; 7:376. PMC: 4811886. DOI: 10.3389/fpls.2016.00376. View

Bray N, Pimentel H, Melsted P, Pachter L . Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016; 34(5):525-7. DOI: 10.1038/nbt.3519. View

Ma N, Tan H, Liu X, Xue J, Li Y, Gao J . Transcriptional regulation of ethylene receptor and CTR genes involved in ethylene-induced flower opening in cut rose (Rosa hybrida) cv. Samantha. J Exp Bot. 2006; 57(11):2763-73. DOI: 10.1093/jxb/erl033. View

Niu L, Lu F, Pei Y, Liu C, Cao X . Regulation of flowering time by the protein arginine methyltransferase AtPRMT10. EMBO Rep. 2007; 8(12):1190-5. PMC: 2267234. DOI: 10.1038/sj.embor.7401111. View

Genschik P, Marrocco K, Bach L, Noir S, Criqui M . Selective protein degradation: a rheostat to modulate cell-cycle phase transitions. J Exp Bot. 2013; 65(10):2603-15. DOI: 10.1093/jxb/ert426. View

Chen Q, Chen X, Wang Q, Zhang F, Lou Z, Zhang Q . Structural basis of a histone H3 lysine 4 demethylase required for stem elongation in rice. PLoS Genet. 2013; 9(1):e1003239. PMC: 3554631. DOI: 10.1371/journal.pgen.1003239. View

Li Z, Jiang G, Liu X, Ding X, Zhang D, Wang X . Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato. New Phytol. 2020; 227(4):1138-1156. DOI: 10.1111/nph.16590. View

10.

Wang H, Huang Z, Xia L, Feng Q, Erdjument-Bromage H, Strahl B . Methylation of histone H4 at arginine 3 facilitating transcriptional activation by nuclear hormone receptor. Science. 2001; 293(5531):853-7. DOI: 10.1126/science.1060781. View

11.

Li W, Yan J, Wang S, Wang Q, Wang C, Li Z . Genome-wide analysis of SET-domain group histone methyltransferases in apple reveals their role in development and stress responses. BMC Genomics. 2021; 22(1):283. PMC: 8054418. DOI: 10.1186/s12864-021-07596-0. View

12.

Lescot M, Dehais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y . PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2001; 30(1):325-7. PMC: 99092. DOI: 10.1093/nar/30.1.325. View

13.

Sun Q, Zhou D . Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development. Proc Natl Acad Sci U S A. 2008; 105(36):13679-84. PMC: 2533249. DOI: 10.1073/pnas.0805901105. View

14.

Kouzarides T . Chromatin modifications and their function. Cell. 2007; 128(4):693-705. DOI: 10.1016/j.cell.2007.02.005. View

15.

Kenchanmane Raju S, Ledford M, Niederhuth C . DNA methylation signatures of duplicate gene evolution in angiosperms. Plant Physiol. 2023; 192(4):2883-2901. PMC: 10400039. DOI: 10.1093/plphys/kiad220. View

16.

Sandve S, Rohlfs R, Hvidsten T . Subfunctionalization versus neofunctionalization after whole-genome duplication. Nat Genet. 2018; 50(7):908-909. DOI: 10.1038/s41588-018-0162-4. View

17.

Hurst L . The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 2002; 18(9):486. DOI: 10.1016/s0168-9525(02)02722-1. View

18.

Liu C, Lu F, Cui X, Cao X . Histone methylation in higher plants. Annu Rev Plant Biol. 2010; 61:395-420. DOI: 10.1146/annurev.arplant.043008.091939. View

19.

Chen C, Chen H, Zhang Y, Thomas H, Frank M, He Y . TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol Plant. 2020; 13(8):1194-1202. DOI: 10.1016/j.molp.2020.06.009. View

20.

Da L, Liu Y, Yang J, Tian T, She J, Ma X . AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. Front Plant Sci. 2019; 10:1333. PMC: 6817610. DOI: 10.3389/fpls.2019.01333. View