School of Biosciences

Image of Rupert Fray

Rupert Fray

Professor of Epitranscriptomics, Faculty of Science


  • workRoom A04 Plant Sciences
    Sutton Bonington Campus
    Sutton Bonington
    LE12 5RD
  • work0115 951 6371
  • fax0115 951 6334


Professor of Epitranscriptomics

Rupert's main research interest is the study of messenger RNA (mRNA) methylation in plants and other eukaryotes. His group studies the enzymes involved in the synthesis of N6 methyladenosine, the mRNAs that are targeted for methylation, the consequences of this methylation and the proteins that recognise the modified nucleotide.

He also has a long standing interest in synthetic biology approaches to crop improvement with research areas including the manipulation of plant-microbe interactions through "quorum sensing", chloroplast transformation systems and the production of taxanes in heterologous plant systems.

Expertise Summary

Detection and quantification of modified nucleotides in mRNA.

Manipulation of metabolic pathways for the production of novel products in transgenic plants.

Teaching Summary

Rupert convenes unergraduate and post graduate modules in" Molecular Pharming" and Plant "Cell Signalling" .

In addition he contributes lectures to "Plant Science", "Plant Biotechnology", "Resource Capture", "Sex Flowers and Biotechnology", "Genetics".

Research Summary

My Group studies the role of post-transcriptional adenosine methylation in mRNA. N6-methyladenosine (m6A) is a ubiquitous modification present in the messenger RNA of many eukaryotes and… read more

Selected Publications

Current Research

My Group studies the role of post-transcriptional adenosine methylation in mRNA. N6-methyladenosine (m6A) is a ubiquitous modification present in the messenger RNA of many eukaryotes and nuclear-replicating viruses. Unlike cap methylation, it can be found throughout the message and has been detected in coding, non-coding and intron sequences. However, despite its widespread occurrence, its function has remained a mystery since its discovery over 30 years ago. This modification is common in most eukaryotes and in plants it appears to be essential. Adenosines in the sequence context GAC or AAC can become methylated, but the average frequency of methylated adenosine is only once per 500 nucleotides. However, not all mRNAs contain the modification, indicating that additional features must be required for specificity. We have recently shown that m6A levels in Arabidopsis mRNA vary between different plant tissues. In addition, MTA, the Arabidopsis homologue of the human mRNA methylase, is required for embryo development and interacts in vitro and in vivo with AtFIP37, a plant homologue of the Drosophila protein female lethal 2 D and of human WILMS' TUMOUR 1-ASSOCIATING PROTEIN.

Previously I held a BBSRC Sir David Philips Research Fellowship which supported my research concerning the role of "quorum sensing" during interactions between plants and various gram negative bacteria. Some work in this area continues within the Group.


Wang D, Samsulrizal NH, Yan C, Allcock NS, Craigon J, Blanco-Ulate B, Ortega-Salazar I, Marcus SE, Bagheri HM, Perez Fons L, Fraser PD, Foster T, Fray R, Knox JP, Seymour GB. (2019) Characterization of CRISPR Mutants Targeting Genes Modulating Pectin Degradation in Ripening Tomato. Plant Physiol. 179: 544-557.

Jantsch MF et al. (2018)Positioning Europe for the EPITRANSCRIPTOMICS challenge. RNA Biol. 15:829-831.

Anderson SJ, Kramer MC, Gosai SJ, Yu X, Vandivier LE, Nelson ADL, Anderson ZD, Beilstein MA, Fray RG, Lyons E, Gregory BD. (2018) N(6)-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis. Cell Rep. 25:1146-1157.

Růžička K., Zhang M, Campilho A., Bodi Z., Kashif M., Saleh M, Eeckhout D, El-Showk S., Li H., Zhong S., De Jaeger G., Mongan NP., Hejátko J., Helariutta Y., Fray RG. (2017) Identification of Factors Required for m6A mRNA Methylation in Arabidopsis Reveals a Role for the Conserved E3 Ubiquitin Ligase HAKAI. New Phytologist. 215; 157-172.

Bodi Z, Fray RG. (2017) Detection and Quantification of N (6)-Methyladenosine in Messenger RNA by TLC. Methods Mol Biol.1562:79-87.

Haussmann IU., Bodi Z., Sanchezmoran E., Mongan NP., Archer N., Fray RG., Soller M. (2016) m6A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination. Nature 540; 301-304

Uluisik S., et al. (2016) Genetic improvement of tomato by targeted control of fruit softening. Nature Biotechnology 34; 950-952

Chew BL., Fisk ID., Fray RG., Tucker GA., Bodi Z., Feerguson A., Xia W., Seymour GB. (2016) The effect of adenosine monophosphate deaminase overexpression on the accumulation of umami-related metabolites in tomatoes. Plant Cell Rep. doi:10.1007/s00299-016-2058-z

Barton NA., Marsh BJ., Lewis W., Narraidoo N., Seymour GB., Fray R., Hayes, CJ. (2016) Accessing low-oxidation state taxanes: is taxadiene-4(5)-epoxide on the taxol biosynthetic pathway? Chemical Science 7; 3102-3107

Bodi Z., Bottley A., Archer N., May ST., Fray RG. (2015) Yeast m(6)A Methylated mRNAs Are Enriched on Translating Ribosomes during Meiosis, and under Rapamycin Treatment. PLOS ONE 10 Issue: 7 Article Number: e0132090.

Pan Y, et al. (2013) Network Inference Analysis Identifies an APRR2-Like Gene Linked to Pigment Accumulation in Tomato and Pepper Fruits. Plant Physiology 161:1476-1485

Bodi Z., Zhong S., Mehra S., Song J., Graham N., Li H., May S. and Fray RG., 2012. Adenosine methylation in Arabidopsis mRNA is associated with the 3′ end and reduced levels cause developmental defects. Frontiers in Plant Science | Plant Genetics and Genomics: Front. Plant Sci. 3:48.. Volume 3(Article 48 20

Kruse, S., Zhong, S, Bodi, Z., Button, J., Alcocer, M.J.C., Hayes, C. and Fray, R., 2011. A novel synthesis and detection method for cap-associated adenosine modifications in mouse mRNA Scientific Reports. DOI: 10.1038/srep00126.

Ó Lochlainn S., Bowen HC, Fray RG, Hammond JP, King GJ, White PJ, Graham NS, Broadley MR (2011) Tandem Quadruplication of HMA4 in the Zinc (Zn) and Cadmium (Cd) Hyperaccumulator Noccaea caerulescens PLoS ONE 6(3): e17814.

Ó Lochlainn S, Fray RG, Hammond JP, King GJ, White PJ, Young SD, Broadley MR (2011) Generation of nonvernal-obligate, faster-cycling Noccaea caerulescens lines through fast neutron mutagenesis. New Phytologist 189; 409-414.

Bodi Z., Button JD., Grierson D, Fray RG. (2010) Yeast targets for mRNA methylation. Nucleic Acids Res 38(16), 5327-35

Kovacs, K., Fray, R.G., Tikunov Y., Graham, N., Bradley, G. Seymour, G.B., Bovy, A.G. and Grierson D (2009).Effect of tomato pleiotropic ripening mutations on flavour volatile biosynthesis. Phytochemistry 70: 1003-1008.

Kovács K., Hill PJ., Grierson D., Dodd CER., Pamfil D., Fray RG. (2009) Development of a novel inducible bioluminescent and antibiotic resistance tagging system and its use to investigate the role of antibiotic production by Pectobacterium carotovorum ssp. carotovorum during potato tuber infection European Journal of Plant Pathology 125: 655-664.

M. R. Broadley, MR., White, PJ., Hammond, JP., Graham, NS., Bowen, HC., Emmerson, ZF., Fray, RG., Iannetta, PPM., McNicol, JW. and May, ST. (2008) Evidence of neutral transcriptome evolution in plants. New Phytologist 180 in press and on line 10.1111/j.1469-8137.2008.02640.x(2008).

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 available on line Zhong, S., Lin, Z., Fray, RG., Grierson, D., (2007) Improved Gateway Vectors for Fluorescent Protein Tagging. Transgenic Research. Accepted and available on line

Jaffé , B., Kovács, K., Andras, C., Bódi, Z., Liu, Z., Fray R.G. (2008) Methylation of chloroplast DNA does not affect viability and maternal inheritance in tobacco and may provide a strategy towards transgene containment. Plant Cell Reports 27 1377-1384.

Barriuso, J., Solano, B.R., Fray, R.G., Camara, M., Hartmann, A., Manero, F.J.G. (2008) Transgenic tomato plants alter quorum sensing in plant growth-promoting rhizobacteria. Plant Biotechnology Journal 6 442-452.

Fray RG. (2006) Thymus desoxypentose nucleic acid sixty years on. Society for Experimental Biology.

Kovacs K., Zhang L., Linforth RS, Whittaker B., Hayes CJ., Fray R.G. (2007) Redirection of carotenoid metabolism for the efficient production of taxadiene [taxa-4(5),11(12)-diene] in transgenic tomato fruit. Transgenic Research 16 (1): 121-126.

Scott RA., Weil J., Le PT., Williams P., Fray RG., von Bodman SB, Savka MA. (2006) Long- and short-chain plant-produced bacterial N-acyl-homoserine lactones become components of phyllosphere, rhizosphere, and soil. Molecular Plant Microbe Interactions 19 (3): 227-239.

d'Angelo-Picard C., Faure D., Carlier A., Uroz S., Raffoux A., Fray RG., Dessaux Y. (2004) Bacterial populations in the rhizosphere of tobacco plants producing the quorum-sensing signals hexanoyl-homoserine lactone and 3-oxo-hexanoyl-homoserine lactone. FEMS Microbiology Ecology 51 (1): 19-29.

Waters, MT., Fray, RG., Pyke, KA. (2004) Stromule formation is dependent upon plastid size, plastid differentiation status and the density of plastids within the cell. Plant Journal 39 (4): 655-667.

Toth, IK., Newton, JA., Hyman, LJ., Lees, AK., Daykin, M., Ortori, C., Williams, P., Fray, RG. (2004) Potato plants genetically modified to produce N-acylhomoserine lactones increase susceptibility to soft rot erwiniae. Molecular Plant Microbe Interactions 17 880-888

Newton J., Fray, R. (2004) Integration of environmental and host-derived signals with quorum sensing during plant-microbe interactions. Cellular Microbiology 6 (3): 213-227.

Carlier, A., Uroz, S., Smadja, B., Fray, R., Latour, X., Dessaux, Y., Faure, D. (2003) The Ti plasmid of Agrobacterium tumefaciens harbors an attM paralogous gene, aiiB, also encoding N-acyl homoserine lactonase activity. Applied and Environmental Microbiology 69: 4989-4993

Fray, R.G. (2002) Altering plant-microbe interaction through artificially manipulating bacterial quorum sensing. Annals of Botany 89: 245-253.

Hackett, RM., Ho, CW., Lin, ZF., Foote, HCC., Fray, RG., Grierson, D. (2000) Antisense inhibition of the Nr gene restores normal ripening to the tomato Never-ripe mutant, consistent with the ethylene receptor-inhibition model. Plant Physiology 124 (3): 1079-1085.

Fray, RG., Throup, JP., Daykin, M., Wallace, A., Williams, P., Stewart, GSAB., Grierson, D. (1999) Plants genetically modified to produce N-acylhomoserine lactones communicate with bacteria. Nature Biotechnology 17 1017-1020.

Barry, CS.., Blume, B., Hamilton, H., Fray, R., Payton, S., Alpuche-Solis, A., Grierson, D. (1997) Regulation of ethylene synthesis and perception in tomato and its control using gene technology. In: Biology and biotechnology of the plant hormone ethylene. Kluwer Academic Publishers, London.

Fray,RG., Wallace, AD., Fraser, PD., Valero, D., Hedden, P., Bramley, PM., Grierson, D. (1995) Constitutive expression of a fruit phytoene synthase gene in transgenic tomatoes causes dwarfism by redirecting metabolites from the gibberellin pathway. The Plant Journal 8 693-701.

Payton, S., Fray, RG., Brown, S., Grierson, D.. (1995) ethylene receptor expression is regulated during fruit ripening, flower senescence and abscission. Plant Molecular Biology 32 1237-1241.

Fray, RG., Hamilton, AJ., Grierson, D., Davey,MR., Blackhall, NW. (1995) Use of gene silencing to probe carotenoid gene expression in tomato. In: Lycett G.W., Grierson D. and Tucker G. (eds) Mechanisms and applications of gene silencing. Nottingham University press.

Hamilton, AJ., Fray, RG., Grierson D. (1995) Sense and antisense inactivation of fruit ripening genes in tomato. In: Meyer P. (ed) Gene silencing in higher plants and related phenomena in other eukaryotes. Current Topics in Microbiology and Immunology 197: 77-89

Fray, RG., Wallace, AD., Grierson, D., Lycett, GW. (1994) Nucleotide sequence and expression of a ripening and water stress-related cDNA from tomato with homology to the MIP class of membrane channel proteins. Plant Molecular Biology 24 539-543.

Grierson, D., Fray, RG. (1994) Control of ripening in transgenic tomatoes. Euphytica 79 251-263.

Fray, RG., Grierson, D. (1993) Molecular genetics of tomato fruit ripening. Trends in Genetics 9 438-443.

Fray, RG., Grierson, D (1993) Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequencing, complementation and co-suppression. Plant Molecular Biology 22 589-602.

Seymour, GB., Fray, RG., Hill, P., Tucker, GA. (1993) Down-regulation of two non-homologous endogenous tomato genes with a single chimaeric sense gene construct. Plant Molecular Biology 23 1-9.

Grierson, D., Fray, RG., Hamilton, AJ., Smith, CJS., Watson, CF. (1991) Does co-suppression of sense genes in transgenic plants involve antisense RNA? Trends in Biotechnology 9 122-123.

Fray, RG., Lycett, GW., Grierson, D. (1990) Nucleotide sequence of a heat-shock and ripening-related cDNA from tomato. Nucleic Acids Research 18 7148

Zsuzsanna Bodi, James D. Button, Donald Grierson and Rupert G. Fray (2010) Yeast targets for mRNA methylation. Nucleic Acids Research 38(16):5327-5335

Katalin Kovács, Philip J. Hill, Donald Grierson, Christine E.R. Dodd, Doru Pamfil, Rupert G. Fray. (2009) Development of a novel inducible bioluminescent and antibiotic resistance tagging system and its use to investigate the role of antibiotic production by Pectobacterium carotovorum ssp. carotovorum during potato tuber infection. European Journal of Plant Pathology 125, Issue 4 (2009), Page 655-664.

Katalin Kovács, Rupert G. Fray, Yury Tikunov, Neil Graham, Glyn Bradley, Graham B. Seymour, Arnaud G. Bovy and Donald Grierson (2009) Effect of tomato pleiotropic ripening mutations on flavour volatile biosynthesis Phytochemistry 70 1003-1008

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University of Nottingham
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LE12 5RD, UK

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