Group leader: Elena Caro Bernat - Assistant Professor
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Stable and high expression of transgenes is essential for the development of any genetically engineered crop, whether its purpose is to produce pharmaceutical or industrial compounds, increased value grain or a pest resistant variety to produce food, feed, or fiber. The low expression of transgenes and the high variability amongst transgenic lines due to gene silencing is nowadays a big challenge for plant molecular farming, plant synthetic biology and the development of new genetically modified crops.

RNAi pathways are responsible for the silencing of transgenes as a result of the activation of defense mechanisms of the plant evolved to confront invasive nucleic acids such as transposons and viruses.

In our lab, we have basic research projects that aim to address how plants distinguish “self” from “non-self” nucleic acids, what are the signals in transgenes that license the silencing response and how can they be avoided in the generation of new transgenic plants.

We also have applied biotechnology projects since we are part of an initiative led by Prof. Luis Rubio at the Technical University of Madrid (UPM) to investigate the transfer of nitrogen fixation genes to plants. This research program, for which the Bill & Melinda Gates Foundation has awarded funding of $5 million, 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. Development of epigenetic markers related to seed germination (EPI-SEED). Programa propio de I+D+i de la UPM. Ayuda dirigida a jóvenes investigadores doctores para fortalecer sus planes de investigación
  2. BNF-Cereals Phase II (2016-2020). Bill & Melinda Gates Foundation.
  3. Silenciamiento génico en aplicaciones de biotecnología vegetal (2015-2017). Programa Estatal de Investigación Científica y Técnica de Excelencia (BIO2014-58789-P).


Representative Publications

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".