The plant response to high CO
Arabidopsis
DNA methylation
elevated CO2
epigenetics
mechanism
moss
phenotyping
transgenerational
Journal
The New phytologist
ISSN: 1469-8137
Titre abrégé: New Phytol
Pays: England
ID NLM: 9882884
Informations de publication
Date de publication:
06 2023
06 2023
Historique:
received:
26
12
2022
accepted:
07
03
2023
medline:
19
5
2023
pubmed:
16
3
2023
entrez:
15
3
2023
Statut:
ppublish
Résumé
Plant responses to abiotic environmental challenges are known to have lasting effects on the plant beyond the initial stress exposure. Some of these lasting effects are transgenerational, affecting the next generation. The plant response to elevated carbon dioxide (CO
Substances chimiques
Carbon Dioxide
142M471B3J
Arabidopsis Proteins
0
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2427-2439Subventions
Organisme : National Science Foundation
ID : EF-1921728
Informations de copyright
© 2023 The Authors New Phytologist © 2023 New Phytologist Foundation.
Références
Ainsworth EA, Long SP. 2021. 30 years of free-air carbon dioxide enrichment (FACE): what have we learned about future crop productivity and its potential for adaptation? Global Change Biology 27: 27-49.
Annacondia ML, Markovic D, Reig-Valiente JL, Scaltsoyiannes V, Pieterse CMJ, Ninkovic V, Slotkin RK, Martinez G. 2021. Aphid feeding induces the relaxation of epigenetic control and the associated regulation of the defense response in Arabidopsis. New Phytologist 230: 1185-1200.
Baulcombe DC, Dean C. 2014. Epigenetic regulation in plant responses to the environment. Cold Spring Harbor Perspectives in Biology 6: a019471.
Bäurle I. 2016. Plant heat adaptation: priming in response to heat stress. F1000Research 5: 694.
Bäurle I, Trindade I. 2020. Chromatin regulation of somatic abiotic stress memory. Journal of Experimental Botany 71: 5269-5279.
Bewick AJ, Schmitz RJ. 2017. Gene body DNA methylation in plants. Current Opinion in Plant Biology 36: 103-110.
Bezemer TM, Thompson LJ, Jones TH. 2004. Poa annua shows inter-generational differences in response to elevated CO2. Global Change Biology 4: 687-691.
Böwer F, Schnittger A. 2021. How to switch from mitosis to meiosis: regulation of germline entry in plants. Annual Review of Genetics 55: 1-26.
Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE. 2003. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Current Biology 13: 2212-2217.
Cao X, Jacobsen SE. 2002. Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proceedings of the National Academy of Sciences, USA 99: 16491-16498.
Castellanos RU, Friedrich T, Petrovic N, Altmann S, Brzezinka K, Gorka M, Graf A, Bäurle I. 2020. FORGETTER2 protein phosphatase and phospholipase D modulate heat stress memory in Arabidopsis. The Plant Journal 104: 7-17.
Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one Fastq preprocessor. Bioinformatics 34: i884-i890.
Chen Y, Müller F, Rieu I, Winter P. 2016. Epigenetic events in plant male germ cell heat stress responses. Plant Reproduction 29: 21-29.
Daxinger L, Kanno T, Bucher E, van der Winden J, Naumann U, Matzke AJM, Matzke M. 2009. A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation. EMBO Journal 28: 48-57.
Ding Y, Fromm M, Avramova Z. 2012. Multiple exposures to drought “train” transcriptional responses in Arabidopsis. Nature Communications 3: 740.
Du J, Johnson LM, Jacobsen SE, Patel DJ. 2015. DNA methylation pathways and their crosstalk with histone methylation. Nature Reviews Molecular Cell Biology 16: 519-532.
Ebbs ML, Bender J. 2006. Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell 18: 1166-1176.
Erdmann RM, Picard CL. 2020. RNA-directed DNA methylation. PLoS Genetics 16: e1009034.
Fahlgren N, Feldman M, Gehan MA, Wilson MS, Shyu C, Bryant DW, Hill ST, McEntee CJ, Warnasooriya SN, Kumar I et al. 2015. A versatile phenotyping system and analytics platform reveals diverse temporal responses to water availability in Setaria. Molecular Plant 8: 1520-1535.
Feng S, Zhong Z, Wang M, Jacobsen SE. 2020. Efficient and accurate determination of genome-wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl sequencing. Epigenetics & Chromatin 13: 42.
Gehan MA, Fahlgren N, Abbasi A, Berry JC, Callen ST, Chavez L, Doust AN, Feldman MJ, Gilbert KB, Hodge JG et al. 2017. PlantCV v.2: image analysis software for high-throughput plant phenotyping. PeerJ 5: e4088.
Golzarian MR, Frick RA, Rajendran K, Berger B, Roy S, Tester M, Lun DS. 2011. Accurate inference of shoot biomass from high-throughput images of cereal plants. Plant Methods 7: 2.
Harris BJ, Clark JW, Schrempf D, Szöllősi GJ, Donoghue PCJ, Hetherington AM, Williams TA. 2022. Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants. Nature Ecology & Evolution 6: 1634-1643.
Heard E, Martienssen RA. 2014. Transgenerational epigenetic inheritance: myths and mechanisms. Cell 157: 95-109.
Hu L, Li N, Xu C, Zhong S, Lin X, Yang J, Zhou T, Yuliang A, Wu Y, Chen Y-R et al. 2014. Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality. Proceedings of the National Academy of Sciences, USA 111: 10642-10647.
Hu S, Chen W, Tong K, Wang Y, Jing L, Wang Y, Yang L. 2022. Response of rice growth and leaf physiology to elevated CO2 concentrations: a meta-analysis of 20-year FACE studies. Science of the Total Environment 807: 151017.
Jackson JP, Lindroth AM, Cao X, Jacobsen SE. 2002. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416: 556-560.
Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T. 2003. Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Current Biology 13: 421-426.
Keeling RF, Keeling CD. 2017. Atmospheric monthly in situ CO2 data - Mauna Loa Observatory, Hawaii. In: Scripps CO2 program data [Data set]. UC San Diego Library Digital Collections. doi: 10.6075/J08W3BHW.
Kimball BA. 2016. Crop responses to elevated CO2 and interactions with H2O, N, and temperature. Current Opinion in Plant Biology 31: 36-43.
Lämke J, Bäurle I. 2017. Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants. Genome Biology 18: 124.
Lau JA, Peiffer J, Reich PB, Tiffin P. 2008. Transgenerational effects of global environmental change: long-term CO2 and nitrogen treatments influence offspring growth response to elevated CO2. Oecologia 158: 141-150.
Lee D-E, Lee I-J, Han O, Baik M-G, Han S-S, Back K. 2004. Pathogen resistance of transgenic rice plants expressing mitogen-activated protein kinase 1, MK1, from Capsicum annuum. Molecules and Cells 17: 81-85.
Li Y, Li X, Yu J, Liu F. 2017. Effect of the transgenerational exposure to elevated CO2 on the drought response of winter wheat: stomatal control and water use efficiency. Environmental and Experimental Botany 136: 78-84.
Liu H, Able AJ, Able JA. 2021. Priming crops for the future: rewiring stress memory. Trends in Plant Science 27: 699-716.
López M-E, Roquis D, Becker C, Denoyes B, Bucher E. 2022. DNA methylation dynamics during stress response in woodland strawberry (Fragaria vesca). Horticulture Research 9: uhac174.
Lv C, Hu Z, Wei J, Wang Y. 2022. Transgenerational effects of elevated CO2 on rice photosynthesis and grain yield. Plant Molecular Biology 110: 413-424.
Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife 6: e30674.
Mathieu O, Reinders J, Čaikovski M, Smathajitt C, Paszkowski J. 2007. Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130: 851-862.
McCue AD, Nuthikattu S, Reeder SH, Slotkin RK. 2012. Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA. PLoS Genetics 8: e1002474.
Mirouze M, Reinders J, Bucher E, Nishimura T, Schneeberger K, Ossowski S, Cao J, Weigel D, Paszkowski J, Mathieu O. 2009. Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461: 427-430.
Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T. 2001. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411: 212-214.
Panda K, Ji L, Neumann DA, Daron J, Schmitz RJ, Slotkin RK. 2016. Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. Genome Biology 17: 170.
Perrella G, Bäurle I, Zanten M. 2022. Epigenetic regulation of thermomorphogenesis and heat stress tolerance. New Phytologist 234: 1144-1160.
Perroud P, Cove DJ, Quatrano RS, McDaniel SF. 2011. An experimental method to facilitate the identification of hybrid sporophytes in the moss Physcomitrella patens using fluorescent tagged lines. New Phytologist 191: 301-306.
Pikaard CS, Haag JR, Ream T, Wierzbicki AT. 2008. Roles of RNA polymerase IV in gene silencing. Trends in Plant Science 13: 390-397.
Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research 44: W160-W165.
Saban JM, Watson-Lazowski A, Chapman MA, Taylor G. 2020. The methylome is altered for plants in a high CO2 world: insights into the response of a wild plant population to multigenerational exposure to elevated atmospheric [CO2]. Global Change Biology 26: 6474-6492.
Saze H, Scheid OM, Paszkowski J. 2003. Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nature Genetics 34: 65-69.
Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H et al. 2015. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 523: 212-216.
Schwalm CR, Glendon S, Duffy PB. 2020. RCP8.5 tracks cumulative CO2 emissions. Proceedings of the National Academy of Sciences, USA 117: 19656-19657.
Sequeira-Mendes J, Aragüez I, Peiró R, Mendez-Giraldez R, Zhang X, Jacobsen SE, Bastolla U, Gutierrez C. 2014. The functional topography of the Arabidopsis genome is organized in a reduced number of linear motifs of chromatin states. Plant Cell 26: 2351-2366.
Shoresh M, Gal-On A, Leibman D, Chet I. 2006. Characterization of a mitogen-activated protein kinase gene from cucumber required for trichoderma-conferred plant resistance. Plant Physiology 142: 1169-1179.
Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L, Patel DJ, Jacobsen SE. 2014. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nature Structural & Molecular Biology 21: 64-72.
Stroud H, Greenberg MVC, Feng S, Bernatavichute YV, Jacobsen SE. 2013. Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152: 352-364.
Tomimatsu H, Tang Y. 2016. Effects of high CO2 levels on dynamic photosynthesis: carbon gain, mechanisms, and environmental interactions. Journal of Plant Research 129: 365-377.
Tovar JC, Hoyer JS, Lin A, Tielking A, Callen ST, Castillo SE, Miller M, Tessman M, Fahlgren N, Carrington JC et al. 2018. Raspberry Pi-powered imaging for plant phenotyping. Applications in Plant Sciences 6: e1031.
Villagómez-Aranda AL, Feregrino-Pérez AA, García-Ortega LF, González-Chavira MM, Torres-Pacheco I, Guevara-González RG. 2022. Activating stress memory: eustressors as potential tools for plant breeding. Plant Cell Reports 41: 1481-1498.
Wibowo A, Becker C, Marconi G, Durr J, Price J, Hagmann J, Papareddy R, Putra H, Kageyama J, Becker J et al. 2016. Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity. eLife 5: e13546.
Xie X, Shippen DE. 2018. DDM1 guards against telomere truncation in Arabidopsis. Plant Cell Reports 37: 501-513.
Yiotis C, McElwain JC, Osborne BA. 2020. Increased productivity of ryegrass grown at elevated CO2 is dependent on tillering and leaf area development rather than leaf-level photosynthesis. Journal of Experimental Botany 72: eraa584.
Yu L, Dong H, Huang Z, Korpelainen H, Li C. 2021. Elevated CO2 causes different growth stimulation, water- and nitrogen-use efficiencies, and leaf ultrastructure responses in two conifer species under intra- and interspecific competition. Tree Physiology 41: 2082-2095.
Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153: 193-205.
Zhang H, Lang Z, Zhu J-K. 2018. Dynamics and function of DNA methylation in plants. Nature Reviews Molecular Cell Biology 19: 489-506.