Normal development in plants and animals depends on the precise regulation of gene expression, which includes a wide range of mechanisms used by cells to increase or decrease the production of specific gene products. One of such mechanisms is RNA silencing, an epigenetic modification leading to the stable inactivation of previously active genes. In plants, it also provides sequence-specific regulation during development and reproduction, and enables adaptability in response to biotic and abiotic stresses.

Elena Caro and Juan Carlos del Pozo direct a joint research line on the study of the role of epigenetics, and more specifically, small RNAs and DNA methylation, in the response to abiotic stresses like heat and phosphorous deficit. This work is mainly performed in Arabidopsis, but has great potential for translatability to crops since the investigations are performed using the D-root and TGRooZ devices, that reproduce field conditions, maintaining roots in the dark and in a decreasing gradient of temperature.

RNA silencing, apart from controlling endogenous genes expression, is also efficient for the control of viruses as well as repetitive and transposable elements, indicating that this mechanism works as a genetic defense system against exogenous nucleic acids. Transgenes resemble these cellular invaders, and are also targets of host reactions based on RNA silencing. In fact, although the genetic transformation of plants has become an essential tool for plant biology research and biotechnological applications, its potential is significantly hindered by the fact that transgene expression is often low and highly variable due to transgene silencing. Our lab tries to understand silencing triggers and circumvent this limitation for SynBio projects.

Elena Caro collaborates in Prof. Luis Rubio’s project to investigate the transfer of nitrogen fixation genes from bacteria to plants (NFIX), applying her knowledge on (trans)gene expression regulation in plants. This research program, for which the Bill & Melinda Gates Foundation has awarded funding of more than $12 million since 2012, aims to obtain cereals with minimum requirements of nitrogen fertilizers that will produce higher and more consistent returns on their crops.

FIGURE: Generation of a tool to search for construct features that promote/avoid gene silencing


  1. Effect of global warming on plant nutrition, root growth and microbiome association (PID2020-113479RB-I00). 2021-2024. Programa Estatal de Proyectos de I+D+i Retos Investigación, Ministerio de Ciencia e Innovación. IP: Juan Carlos del Pozo; Co-IP: Elena Caro.
  2. EMMA: Engineering multi-functional microbes for plant-related applications. Missiones CBGP: Severo Ochoa Excellence Program 22-25. IP: Ángel Goñi. Co-IPs: Elena Caro, Alejandro Couce, Manuel Gonzalez-Guerrero, Juan Imperial and Luis M. Rubio.


Representative Publications

Agius, D.R., Kapazoglou, A., Avramidou, E., Baranek, M., Carneros, E., Caro, E., Castiglione, S., Cicatelli, A., Radanovic, A., Ebejer, J.-P., Gackowski, D., Guarino, F., Gulyás, A., Hidvégi, N., Hoenicka, H., Inácio, V., Johannes, F., Karalija, E., Lieberman-Lazarovich, M., Martinelli, F., Maury, S., Mladenov, V., Morais-Cecílio, L., Pecinka, A., Tani, E., Testillano, P.S., Todorov, D., Valledor, L., Vassileva, V. 2023. Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. Frontiers in Plant Science 14. DOI: 10.3389/fpls.2023.1181039

Vergara, Z., Gomez, M.S., Desvoyes, B., Sequeira-Mendes, J., Masoud, K., Costas, C., Noir, S., Caro, E., Mora-Gil, V., Genschik, P., Gutierrez, C. 2023. Distinct roles of Arabidopsis ORC1 proteins in DNA replication and heterochromatic H3K27me1 deposition. Nature Communications 14, 1270. DOI: 10.1038/s41467-023-37024-8

González-García, M.P., Conesa, C.M., Lozano-Enguita, A., Baca-González, V., Simancas, B., Navarro-Neila, S., Sánchez-Bermúdez, M., Salas-González, I., Caro, E., Castrillo, G., del Pozo, J.C. 2022. Temperature changes in the root ecosystem affect plant functionality. Plant Communications 100514. DOI: 10.1016/j.xplc.2022.100514

Montes, N., Cobos, A., Gil-Valle, M., Caro, E., Pagán, I. 2021. Arabidopsis thaliana Genes Associated with Cucumber mosaic virus Virulence and Their Link to Virus Seed Transmission. Microorganisms 9, 692. DOI: 10.3390/microorganisms9040692

Eseverri, Á., Baysal, C., Medina, V., Capell, T., Christou, P., Rubio, L.M., Caro, E. 2020. Transit Peptides From Photosynthesis-Related Proteins Mediate Import of a Marker Protein Into Different Plastid Types and Within Different Species. Frontiers in Plant Science 11, 1474. DOI: 10.3389/fpls.2020.560701

Katsuya-Gaviria, K., Caro, E., Carrillo-Barral, N., Iglesias-Fernández, R. 2020. Reactive Oxygen Species (ROS) and Nucleic Acid Modifications During Seed Dormancy. Plants 9, 679. DOI: 10.3390/plants9060679

Eseverri, Á., López‐Torrejón, G., Jiang, X., Burén, S., Rubio, L.M., Caro, E. 2020. Use of synthetic biology tools to optimize the production of active nitrogenase Fe protein in chloroplasts of tobacco leaf cells. Plant Biotechnology Journal. DOI: 10.1111/pbi.13347

Diezma‐Navas, L., Pérez‐González, A., Artaza, H., Alonso, L., Caro, E., Llave, C., Ruiz‐Ferrer, V. 2019. Crosstalk between epigenetic silencing and infection by tobacco rattle virus in Arabidopsis. Molecular Plant Pathology 20, 1439–1452. DOI: 10.1111/mpp.12850

Baysal, C., Pérez-González, A., Eseverri, Á., Jiang, X., Medina, V., Caro, E., Rubio, L., Christou, P., Zhu, C. 2019. Recognition motifs rather than phylogenetic origin influence the ability of targeting peptides to import nuclear-encoded recombinant proteins into rice mitochondria. Transgenic Research. DOI: 10.1007/s11248-019-00176-9

Pérez-González, A., Caro, E. 2019. Benefits of using genomic insulators flanking transgenes to increase expression and avoid positional effects. Scientific Reports 9, 8474. DOI: 10.1038/s41598-019-44836-6

Pérez-González, A; Eseverri, Á; Caro, E. 2018. "Characterization of Plant Genetic Modifications Using Next-Generation Sequencing", p. 249-259. In S. Singh (ed.), Synthetic Biology: Omics Tools and Their Applications. Springer Singapore, Singapore. DOI: 10.1007/978-981-10-8693-9_13".

Pérez-González, A; Caro, E. 2018. "Effect of transcription terminator usage on the establishment of transgene transcriptional gene silencing". BMC Research Notes. DOI: 10.1186/s13104-018-3649-2".

Pérez-González, A; Kniewel, R; Veldhuizen, M; Verma, HK; Navarro-Rodríguez, M; Rubio, LM; Caro, E. 2017. "Adaptation of the GoldenBraid modular cloning system and creation of a toolkit for the expression of heterologous proteins in yeast mitochondria". BMC Biotechnology. DOI: 10.1186/s12896-017-0393-y".

Pérez-González, A; Caro, E. 2016. "Hindrances to the efficient and stable expression of transgenes in plant synthetic biology approaches", p. 79-89. In S. Singh (ed.), Systems Biology Application in Synthetic Biology. Springer India, New Delhi. DOI: 10.1007/978-81-322-2809-7_7".

Mauri, N; Fernandez-Marcos, M; Costas, C; Desvoyes, B; Pichel, A; Caro, E; Gutierrez, C. 2016. "GEM, a member of the GRAM domain family of proteins, is part of the ABA signaling pathway". Scientific Reports. DOI: 10.1038/srep22660".

Stroud, H; Hale, CJ; Feng, S; Caro, E; Jacob, Y; Michaels, SD; Jacobsen, SE. 2012. "DNA methyltransferases are required to induce heterochromatic re-replication in Arabidopsis". PLoS Genet. DOI: 10.1371/journal.pgen.1002808".

Du, J; Zhong, X; Bernatavichute, Yana V; Stroud, H; Feng, S; Caro, E; Vashisht, Ajay A; Terragni, J; Chin, Hang G; Tu, A; Hetzel, J; Wohlschlegel, James A; Pradhan, S; Patel, Dinshaw J; Jacobsen, Steven E. 2012. "Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants". Cell. DOI: 10.1016/j.cell.2012.07.034".

Caro, E; Stroud, H; Greenberg, MVC; Bernatavichute, YV; Feng, S; Groth, M; Vashisht, AA; Wohlschlegel, J; Jacobsen, SE. 2012. "The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation–independent manner". PLoS Genet. DOI: 10.1371/journal.pgen.1002995".