Epigenetics Group - Detailed - Institute of Genetics and Biotechnology
Epigenetics Group
Epigenetics Group - Detailed
Last modified: 21. April 2023
Introduction of the Research Group
The main research topic of my group is the epigenetic regulation of tomato development and fruit ripening that has both basic research and applied science aspects. The members of the research group are György Szittya (PI), Péter Gyula (post.doc), Tünde Nyikó (post.doc), Anita Sós-Hegedűs (post.doc), Teréz Gorcsa (PhD student) and Tamás Tóth (PhD student).
Tomato is one of the most popular vegetables on the globe and according to a FAO estimation in 2005, it produced 16,9 million tons yield on a total production area of about 290 thousand ha just in the European Union (EU-25). Therefore, tomato has a paramount economic importance as it supports a global food industry in an estimated annual market value of $55 billion. Beside its economic and nutritional importance, tomato is also the principal model to study fleshy fruit development and ripening and to investigate the molecular bases of commercially important traits, such as fruit set, colour, flavour, size and nutritional quality. Ripening in fleshy fruits involves a dramatic metabolic phase change that is under strict genetic, epigenetic and hormonal control. Fruit ripening manifests as a tightly coordinated and regulated set of physiological and biochemical processes that could not be tolerated during other phases of plant development or in other organs. Therefore, it must be limited to the fruit and coordinated with development for optimal effect. Early studies of ripening control revealed the importance of hormones, especially ethylene, in the ripening of climacteric fruits (eg. tomato), whose maturation is associated with dramatically increased respiration in concert with or just preceding an ethylene burst.
Genomic DNA methylation is an important mechanism that influences gene expression, and methylation at promoters is known to inhibit gene transcription. Therefore, it is likely that the active removal of methylation marks is an important mechanism during plant development and plant cell fate reprogramming, leading to the hypomethylation of sites important for DNA–protein interaction and gene expression. It was shown recently that that active DNA demethylation is involved in tomato fruit ripening process.
The tomato genome contains four putative DML genes encoding proteins with characteristic domains of functional DNA demethylase. It was recently demonstrated that repression of the SlDML2 gene expression in transgenic tomato, inhibits fruit DNA demethylation and strongly inhibits the onset and progression of fruit ripening. This demonstrated that SlDML2 is central in mediating the promoter DNA hypomethylation necessary for ripening progression of tomato. We use CRISPR/Cas9 system targeting of cis-regulatory motifs of SlDML2 promoter to engineer fruit ripening variants of tomato. Genome editing driven mutagenesis of SlDML2 promoter creates a continuum of variation for fruit ripening. Selected SlDML2 promoter alleles with altered fruit ripening and shelf life could improve fruit quality traits that could be later used in plant breeding. The increased shelf life has an important economic and environmental protection consequence, since it is a major contributor to the reduction of post-harvest losses.
Summary of the research projects
- Engineering tomato fruit ripening variation by genome editing (PI: György Szittya).
The SlDML2 mediated active DNA demethylation is central to the control of fruit ripening in tomato. We use CRISPR/Cas9 system targeting of cis-regulatory motifs of SlDML2 promoter to engineer fruit ripening variants of tomato. Genome editing driven mutagenesis of SlDML2 promoter created a continuum of variation for fruit ripening. Selected SlDML2 promoter alleles with altered fruit ripening and shelf life could improve fruit quality traits that could be later used in plant breeding.
- Investigation of the epigenetic regulation of tomato fruit ripening, (PI: György Szittya)
The molecular mechanisms how SlDML2 is preferentially targeted to its target genomic loci that regulate fruit ripening are also unknown in crop plants. Therefore, we conduct various transient and transgenic assays to experimentally identify the factors that provide the target selection of SlDML2 in tomato. We hope to identify trans-factors that helps SlDML2 target site recognition.
- Epigenetic factors in tomato development and stress response, (PI: Péter Gyula)The tomato genome encodes four SlDML genes. SlDML2 was shown to play a major role in fruit ripening but the physiological role of the other three SlDMLs is unknown. Our hypothesis is that different SlDMLs may have different or partially overlapping target gene sets, therefore may confer different and partially overlapping functions. We knock-out these genes individually and in every combination as well and test their role during development and stress conditions.
Selected Publications:
- Hamar E., Szaker H.M., Kis A., Dalmadi A., Miloro F., Szittya G., Taller J., Gyula P.*, Csorba T.*, Havelda Z.*. (2020). Genome-wide identification of RNA silencing-related genes and their expressional analysis in response to heat stress in barley (Hordeum vulgare L.). Biomolecules 10, 929; doi:10.3390/biom10060929.
- Sós-Hegedűs, A., Domonkos, Á., Tóth, T., Gyula, P., Kaló P.,* Szittya, G.* (2020). Suppression of NB-LRR Genes by miRNAs Promotes Nitrogen-fixing Nodule Development in Medicago truncatula. Plant Cell Environ., 43(5):1117-1129., https://doi.org/10.1111/pce.13698.
- Tóth, T., Gyula, P., Salamon, P., Kis, S., Sós-Hegedűs, A., Szittya, G.* (2019). Molecular characterization and in vitro synthesis of infectious RNA of a Turnip vein-clearing virus isolated from Alliaria petiolata in Hungary. PLoS ONE, 2019 Oct 24;14(10):e0224398. doi: 10.1371/journal.pone.0224398.
- Medzihradszky, A., Gyula, P., Sós-Hegedűs, A., Szittya, G., Burgyán, J.* (2019). Transcriptome reprogramming in the shoot apical meristem of CymRSV-infected Nicotiana benthamiana plants associates with viral exclusion and the lack of recovery. Molecular Plant Pathology, 20 (12), 1748-1758. doi: 10.1111/mpp.12875.
- Dalmadi, Á., Gyula, P., Bálint, J., Szittya, G., Havelda, Z.* (2019). AGO-unbound cytosolic pool of mature miRNAs in plant cells reveals a novel regulatory step at AGO1 loading. Nucleic Acids Res., Volume 47, Issue 18, 10 October 2019, Pages 9803–9817, pii: gkz690. doi: 10.1093/nar/gkz690
- Gyula, P., Baksa, I., Tóth, T., Mohorianu, I., Dalmay, T., Szittya, G.* (2018). Ambient temperature regulates the expression of a small set of sRNAs influencing plant development through NF-YA2 and YUC2. Plant Cell Environ., 41(10):2404-2417. doi: 10.1111/pce.13355
- Taller, D., Bálint, J., Gyula, P., Nagy, T., Barta, E., Baksa, I., Szittya, G., Taller, J., Havelda, Z.* (2018). Expansion of Capsicum annum fruit is linked to dynamic tissue-specific differential expression of miRNA and siRNA profiles. PLoS ONE, 2018 Jul 25; 13(7):e0200207. doi: 10.1371/journal.pone.0200207.
- Czotter, N., Molnár, J., Szabó, E., Demián, E., Kontra, L., Baksa, I., Szittya, G., Kocsis, L., Deák, T., Bisztray, G., Tusnády, G., Burgyán, J., Várallyay, E.* (2018). NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian vineyards. Microbiol., 9:122. doi: 10.3389/fmicb.2018.00122
- Kis, S., Salamon, P., Kis, V., Szittya, G.* (2017). Molecular characterization of a beet ringspot nepovirus isolated from Begonia ricinifolia in Hungary. Arch Virol., 162:3559-3562. doi: 10.1007/s00705-017-3521-z.
- Baksa, I., Nagy, T., Barta, E., Havelda, Z., Várallyay, E., Silhavy, D., Burgyán, J., Szittya, G.* (2015). Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis. BMC Genomics, 16:1025. doi: 10.1186/s12864-015-2209-6.
Research grants obtained by the Research Group:
Engineering tomato fruit ripening variation by genome editing). (NKFIH OTKA K-129171) (PI: György Szittya, 2018 – 2022)
Investigation of the epigenetic regulation of tomato fruit ripening, (NKFIH OTKA K-134974) (PI: György Szittya, 2020 – 2024)
Epigenetic factors in tomato development and stress response, (NKFIH OTKA FK-137811) (PI: Péter Gyula, 2021-2025)
Deatiled description of the research projects
Engineering tomato fruit ripening variation by genome editing (PI: György Szittya).
Breeding technologies are critical for improving crop production. Crop breeders always require to have access to genetically enhanced breeding lines with value adding performance traits. Enhancing genetic and phenotypic variation in crops that cause subtle changes in quantitative traits are the most valued by breeders. It was shown, in both animals and plants that many of the genetic changes driving evolution, domestication and breeding occurred in cis-regulatory regions. Since they do not alter protein structure, cis-regulatory variants are frequently less pleiotropic and often cause subtle phenotypic change by modifying the timing, pattern or the level of gene expression. Though widely favoured in evolution and domestication, mutations in cis-regulatory elements (CRE) are far from saturated and thus represent an untapped resource for expanding allellic diversity for breeding. The long shelf life of tomato is an important trait for the quality of fleshy fruit, and it is one of the main objectives in breeding programs as it influences fruit marketability. The SlDML2 mediated active DNA demethylation is central to the control of fruit ripening in tomato. We use CRISPR/Cas9 system targeting of cis-regulatory motifs of SlDML2 promoter to engineer fruit ripening variants of tomato. Genome editing driven mutagenesis of SlDML2 promoter created a continuum of variation for fruit ripening. Selected SlDML2 promoter alleles with altered fruit ripening and shelf life could improve fruit quality traits that could be later used in plant breeding. Furthermore it also could shed light on our understanding that which CREs influences fruit ripening in tomato.
Investigation of the epigenetic regulation of tomato fruit ripening, (PI: György Szittya)
Fruit ripening is under strict epigenetic control mediated by changes in DNA methylation levels. SlDML2-mediated DNA demethylation controls this process and as a consequence it is the major determinant of fruit ripening in tomato and also contributes to post-harvest chilling stress response. Although research effort has been made to understand the mechanism and role of tomato SlDML2-mediated DNA demethylation, still many questions remained unanswered. So far only the mRNA level of SlDML2 was monitored in both tomato vegetative tissues and in ripening fruits. This project investigates the spatial and temporal distribution of SlDML2 protein by confocal microscopy during normal development and under different biotic and abiotic stresses. The molecular mechanisms how SlDML2 is preferentially targeted to its target genomic loci that regulate fruit ripening are also unknown in crop plants. Therefore, we conduct various transient and transgenic assays to experimentally identify the factors that provide the target selection of SlDML2 in tomato. During our work, we investigate the effect of cold stress and virus infection on the expression of SlDML2 protein level. We also hope to identify trans-factors that helps SlDML2 target site recognition. We hope that using the gained information, we can facilitate the selection of tomato varieties that can adapt to the changing environment more effectively. We also hope to identify trans-factors that help DML2 target site recognition.
Epigenetic factors in tomato development and stress response, (PI: Péter Gyula)
There are many different tomato variants that respond to environmental stresses differently underlining the role of inherited traits in development and stress response. Besides classical genetic inheritance epigenetics also play a role in plant stress responses and development, including fruit development. The epigenetic inheritance includes methylation of DNA at certain regions in the genome. The methylation status of DNA is dynamically regulated. DNA demethylases play an important role in tomato fruit development among others. The tomato genome encodes four SlDML genes. SlDML2 was shown to play a major role in fruit ripening but the physiological role of the other three SlDMLs is unknown. Our hypothesis is that different SlDMLs may have different or partially overlapping target gene sets, therefore may confer different and partially overlapping functions. We plan to knock-out these genes individually and in every combination as well. The single, double, triple and quadruple mutants may have gradually more severe phenotypes, depending on the condition tested. The key questions are if the four SlDMLs play a role in stress responses and how their function and target gene sets differ or overlap with each other. This knowledge can serve as a basis for the design of molecular markers for breeding projects to find stress-tolerant tomato variants.
Group Members
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Péter Gyula PhD, Senior Research Associate M.Sc.: Molecular Biology and Biotechnology, József Attila University, Faculty of Science, 1999 Phone: +36-28/430-494 / 4154 |
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Tünde Nyikó PhD, Senior Research Associate Phone: +36-28/430-494 / 4154 |
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Szilvia Ráth, Research Associate Phone: +36-28/430-494 |
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Anita Sós-Hegedűs PhD, Senior Research Associate M.Sc.: Biology, Kossuth Lajos University, Faculty of Life Sciences, 1997 Phone: +36-28/430-494 / 4154 |
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Ms. Gorcsa Teréz, Phd student M.Sc.: Biology, University of Szeged, Faculty of Life Sciences, 2018. Phone: +36-28/430-494 / 4154 |
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Tamás Tóth, PhD student M.Sc.: Biology, University of Debrecen, Faculty of Life Sciences, 2016 Phone: +36-28/430-494 / 4154 |
| Alumni: |
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Collaborations at MATE IGB
| Tibor Csorba, PhD | Department of Plant Biotechnology |
| Zoltán Havelda, PhD | Department of Plant Biotechnology |
| Péter Kaló, PhD | Department of Microbiology and Applied Biotechnology |
| János Taller, PhD | Department of Microbiology and Applied Biotechnology |
Hungarian Collaborators
| Éva Várallyay, PhD | Department of Integrated Plant Protection |