Identification and characterization of genes related to m6A modification in kiwifruit using RNA-seq and ATAC-seq
Abstract
N6-methyladenosine (m6A) RNA modification is a conserved mechanism that regulates the fate of RNA across eukaryotic organisms. Despite its significance, a comprehensive analysis of m6A-related genes in non-model plants, such as kiwifruit, is lacking. Here, we identified 36 m6A-related genes in the kiwifruit genome according to homology and phylogenetic inference. We performed bioinformatics and evolutionary analyses of the writer, eraser, and reader families of m6A modification. Reanalysis of public RNA-seq data collected from samples under various biotic and abiotic stresses indicated that most m6A-related genes were remarkably expressed under different conditions. Through construction of gene co-expression networks, we found significant correlations between several m6A-related genes and transcription factors (TFs) as well as receptor-like genes during the development and ripening of kiwifruit. Furthermore, we performed ATAC-seq assays on diverse kiwifruit tissues to investigate the regulatory mechanisms of m6A-related genes. We identified 10 common open chromatin regions that were present in at least two tissues, and these regions might serve as potential binding sites for MADS protein, C2H2 protein, and other predicted TFs. Our study offers comprehensive insights into the gene family of m6A-related components in kiwifruit, which will lay foundation for exploring mechanisms of post-transcriptional regulation involved in development and adaptation of kiwifruit.
References
Alarcón, C.R., Goodarzi, H., Lee, H., Liu, X., Tavazoie, S., Tavazoie, S.F., 2015. HNRNPA2B1 is a mediator of m6A-dependent nuclear RNA processing events. Cell, 162: 1299-1308.
Arribas-Hernández, L., Bressendorff, S., Hansen, M.H., Poulsen, C., Erdmann, S., Brodersen, P., 2018. An m6A-YTH module controls developmental timing and morphogenesis in Arabidopsis. Plant Cell, 30: 952-967.
Bolger, A.M., Lohse, M., Usadel, B., 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30: 2114-2120.
Cantara, W.A., Crain, P.F., Rozenski, J., McCloskey, J.A., Harris, K.A., Zhang, X., Vendeix, F.A., Fabris, D., Agris, P.F., 2010. The RNA modification database, RNAMDB: 2011 update. Nucleic Acids Res, 39: D195-D201.
Capella-Gutiérrez, S., Silla-Martínez, J.M., Gabaldón, T., 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25: 1972-1973.
Chen, C., Chen, H., Zhang, Y., Thomas, H.R., Frank, M.H., He, Y., Xia, R., 2020. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant, 13: 1194-1202.
Danecek, P., Bonfield, J.K., Liddle, J., Marshall, J., Ohan, V., Pollard, M.O., Whitwham, A., Keane, T., McCarthy, S.A., Davies, R.M., 2021. Twelve years of SAMtools and BCFtools. GigaScience, 10: giab008.
Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., Gingeras, T.R., 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29: 15-21.
Duan, H.C., Wei, L.H., Zhang, C., Wang, Y., Chen, L., Lu, Z., Chen, P.R., He, C., Jia, G., 2017. ALKBH10B is an RNA N6-methyladenosine demethylase affecting Arabidopsis floral transition. Plant Cell, 29: 2995-3011.
Fenn, M.A., Giovannoni, J.J., 2021. Phytohormones in fruit development and maturation. Plant J, 105: 446-458.
Hou, N., Li, C., He, J., Liu, Y., Yu, S., Malnoy, M., Tahir, M.M., Xu, L., Ma, F., Guan, Q., 2022. MdMTA-mediated m6A modification enhances drought tolerance by promoting mRNA stability and translation efficiency of genes involved in lignin deposition and oxidative stress. New Phytol, 234: 1294-1314.
Hsu, P.J., Zhu, Y., Ma, H., Guo, Y., Shi, X., Liu, Y., Qi, M., Lu, Z., Shi, H., Wang, J., 2017. YTHDC2 is an N6-methyladenosine binding protein that regulates mammalian spermatogenesis. Cell Res, 27: 1115-1127.
Hu, J., Cai, J., Umme, A., Chen, Y., Xu, T., Kang, H., 2022. Unique features of mRNA m6A methylomes during expansion of tomato (Solanum lycopersicum) fruits. Plant Physiol, 188: 2215-2227.
Huang, Y., Zheng, P., Liu, X., Chen, H., Tu, J., 2021. OseIF3h regulates plant growth and pollen development at translational level presumably through interaction with OsMTA2. Plants, 10: 1101.
Iyer, L.M., Zhang, D., Aravind, L., 2016. Adenine methylation in eukaryotes: apprehending the complex evolutionary history and functional potential of an epigenetic modification. Bioessays, 38: 27-40.
Jia, D.F., Jiang, Z.Q., Fu, H.H., Chen, L., Liao, G.L., He, Y.Q., Huang, C.H., Xu, X.B., 2021. Genome-wide identification and comprehensive analysis of NAC family genes involved in fruit development in kiwifruit (Actinidia). BMC Plant Biol, 21: 44.
Jia, G., Fu, Y., Zhao, X., Dai, Q., Zheng, G., Yang, Y., Yi, C., Lindahl, T., Pan, T., Yang, Y.G., 2011. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol, 7: 885-887.
Kim, J., Shim, S., Lee, H., Seo, P.J., 2020. m6A mRNA modification as a new layer of gene regulation in plants. J Plant Biol, 63: 97-106.
Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S.J., Marra, M.A., 2009. Circos: an information aesthetic for comparative genomics. Genome Res, 19: 1639-1645.
Langmead, B., Salzberg, S.L., 2012. Fast gapped-read alignment with Bowtie2. Nat Methods, 9: 357-359.
Liao, Y., Smyth, G.K., Shi, W., 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30: 923-930.
Liu, J., Yue, Y., Han, D., Wang, X., Fu, Y., Zhang, L., Jia, G., Yu, M., Lu, Z., Deng, X., 2014. A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat Chem Biol, 10: 93-95.
Ma, S.H., He, G.Q., Cheng, Y.Z., Guo, D.L., 2023. Analysis of alternative splicing at different developmental stages of Kyoho grapes with 5-azaC treatment. Acta Hortic Sin, 50: 523-533. (in Chinese)
Martínez-Pérez, M., Aparicio, F., López-Gresa, M.P., Bellés, J.M., Sánchez-Navarro, J.A., Pallás, V., 2017. Arabidopsis m6A demethylase activity modulates viral infection of a plant virus and the m6A abundance in its genomic RNAs. Proc Natl Acad Sci, 114: 10755-10760.
Minh, B.Q., Schmidt, H.A., Chernomor, O., Schrempf, D., Woodhams, M.D., Von, H.A., Lanfear, R., 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol, 37: 1530-1534.
Muhammad, A., Gu, S.C., Zhang, Y.J., Sun, S.H., Li, Z., Bai, D.F., Sun, L.M., Qi, X.J., Zhong, Y.P., Fang, J.B., 2022. Comparative transcriptome and metabolome analysis reveal key regulatory defense networks and genes involved in enhanced salt tolerance of Actinidia (kiwifruit). Hortic Res, 9: uhac189.
O'Malley, R.C., Huang, S.C., Song, L., Lewsey, M.G., Bartlett, A., Nery, J.R., Galli, M., Gallavotti, A., Ecker, J.R., 2016. Cistrome and epicistrome features shape the regulatory DNA landscape. Cell, 165: 1280-1292.
Ping, X.L., Sun, B.F., Wang, L., Xiao, W., Yang, X., Wang, W.J., Adhikari, S., Shi, Y., Lv, Y., Chen, Y.S., 2014. Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res, 24: 177-189.
Ramírez, F., Ryan, D.P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A.S., Heyne, S., Dündar, F., Manke, T., 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res, 44: W160-W165.
Rodríguez, L.D., Lemmon, Z.H., Man, J., Bartlett, M.E., Lippman, Z.B., 2017. Engineering quantitative trait variation for crop improvement by genome editing. Cell, 171: 470-480.
Ross-Innes, C.S., Stark, R., Teschendorff, A.E., Holmes, K.A., Ali, H.R., Dunning, M.J., Brown, G.D., Gojis, O., Ellis, I.O., Green, A.R., 2012. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature, 481: 389-393.
Rozewicki, J., Li, S., Amada, K.M., Standley, D.M., Katoh, K., 2019. MAFFT-DASH: integrated protein sequence and structural alignment. Nucleic Acids Res, 47: W5-W10.
Růžička, K., Zhang, M., Campilho, A., Bodi, Z., Kashif, M., Saleh, M., Eeckhout, D., El-Showk, S., Li, H., Zhong, S., 2017. Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. New Phytol, 215: 157-172.
Schwope, R., Magris, G., Miculan, M., Paparelli, E., Celii, M., Tocci, A., Marroni, F., Fornasiero, A., De Paoli, E., Morgante, M., 2021. Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression. Plant J, 107: 1631-1647.
Scutenaire, J., Deragon, J.M., Jean, V., Benhamed, M., Raynaud, C., Favory, J.J., Merret, R., Bousquet-Antonelli, C., 2018. The YTH domain protein ECT2 is an m6A reader required for normal trichome branching in Arabidopsis. Plant Cell, 30: 986-1005.
Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., Ideker, T., 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res, 13: 2498-2504.
Shao, Y., Wong, C.E., Shen, L., Yu, H., 2021. N6-methyladenosine modification underlies messenger RNA metabolism and plant development. Curr Opin Plant Biol, 63: 102047.
Shen, L., Liang, Z., Gu, X., Chen, Y., Teo, Z., Hou, X., Cai, W., Dedon, P., Liu, L., Yu, H., 2016. N6-methyladenosine RNA modification regulates shoot stem cell fate in Arabidopsis. Dev Cell, 38: 186-200.
Sorrells, T.R., Johnson, A.D., 2015. Making sense of transcription networks. Cell, 161: 714-723.
Sun, J., Bie, X.M., Wang, N., Zhang, X.S., Gao, X.Q., 2020. Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat. BMC Plant Biol, 20: 1-14.
Tang, C., Klukovich, R., Peng, H., Wang, Z., Yu, T., Zhang, Y., Zheng, H., Klungland, A., Yan, W., 2018. ALKBH5-dependent m6A demethylation controls splicing and stability of long 3′-UTR mRNAs in male germ cells. Proc Natl Acad Sci, 115: E325-E333.
Tang, J., Yang, J., Lu, Q., Tang, Q., Chen, S., Jia, G., 2022. The RNA N6-methyladenosine demethylase ALKBH9B modulates ABA responses in Arabidopsis. J Integr Plant Biol, 64: 2361-2373.
Tannenbaum, M., Sarusi-Portuguez, A., Krispil, R., Schwartz, M., Loza, O., Benichou, J.I., Mosquna, A., Hakim, O., 2018. Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq. Plant Methods, 4: 1-12.
Thorvaldsdóttir, H., Robinson, J.T., Mesirov, J.P., 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings Bioinf, 14: 178-192.
Tu, X., Mejía-Guerra, M.K., Valdes, Franco J.A., Tzeng, D., Chu, P.Y., Shen, W., Wei, Y., Dai, X., Li, P., Buckler, E.S., 2020. Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors. Nat Commun, 11: 5089.
Wang, X., Zhao, B.S., Roundtree, I.A., Lu, Z., Han, D., Ma, H., Weng, X., Chen, K., Shi, H., He, C., 2015. N6-methyladenosine modulates messenger RNA translation efficiency. Cell, 161: 1388-1399.
Wang, Y., Tang, H., Debarry, J.D., Tan, X., Li, J., Wang, X., Lee, T.h., Jin, H., Marler, B., Guo, H., 2012. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res, 40: e49.
Wu, R., Li, A., Sun, B., Sun, J.G., Zhang, J., Zhang, T., Chen, Y., Xiao, Y., Gao, Y., Zhang, Q., 2019. A novel m6A reader Prrc2a controls oligodendroglial specification and myelination. Cell Res, 29: 23-41.
Yu, G., Wang, L.G., He, Q.Y., 2015. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics, 31: 2382-2383.
Yue, H., Nie, X., Yan, Z., Wei, N.S., 2019. N6-methyladenosine regulatory machinery in plants: composition, function and evolution. Plant Biotechnol J, 17: 1194-1208.
Yue, Y., Liu, J., Cui, X., Cao, J., Luo, G., Zhang, Z., Cheng, T., Gao, M., Shu, X., Ma, H., 2018. VIRMA mediates preferential m6A mRNA methylation in 3′ UTR and near stop codon and associates with alternative polyadenylation. Cell Discov, 4: 10.
Zhang, F., Zhang, Y.C., Liao, J.Y., Yu, Y., Zhou, Y.F., Feng, Y.Z., Yang, Y.W., Lei, M.Q., Bai, M., Wu, H., 2019. The subunit of RNA N6-methyladenosine methyltransferase OsFIP regulates early degeneration of microspores in rice. PLoS Genet, 15: e1008120.
Zhang, P., Yu, Y., Cao, L., Zhu, G., Wu, W., Guo, Y., Yin, G., Jia, M., 2023. Research progress of m6A methylation modification response to plant biotic and abiotic stresses. Acta Hortic Sin, 50: 1841-1853. (in Chinese)
Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W., 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biol, 9: 1-9.
Zhang, Z., 2022. KaKs_calculator 3.0: calculating selective pressure on coding and non-coding sequences. Dev Reprod Biol, 20: 536-540.
Zheng, G., Dahl, J.A., Niu, Y., Fedorcsak, P., Huang, C.M., Li, C.J., Vågbø, C.B., Shi, Y., Wang, W.L., Song, S.H., 2013. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell, 49: 18-29.
Zheng, H., Sun, X., Li, J., Song, Y., Song, J., Wang, F., Liu, L., Zhang, X., Sui, N., 2021. Analysis of N6-methyladenosine reveals a new important mechanism regulating the salt tolerance of sweet sorghum. Plant Sci, 304: 110801.
Zhong, S., Li, H., Bodi, Z., Button, J., Vespa, L., Herzog, M., Fray, R.G., 2008. MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor. Plant Cell, 20: 1278-1288.
Zhou, L., Gao, G., Tang, R., Wang, W., Wang, Y., Tian, S., Qin, G., 2022. m6A-mediated regulation of crop development and stress responses. Plant Biotechnol J, 20: 1447-1455.
Zhou, L., Tang, R., Li, X., Tian, S., Li, B., Qin, G., 2021. N6-methyladenosine RNA modification regulates strawberry fruit ripening in an ABA-dependent manner. Genome Biol, 22: 1-32.
Zhou, L., Tian, S., Qin, G., 2019. RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening. Genome Biol, 20: 1-23.
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