In plants, small RNA (sRNA)-directed gene silencing pathways control key biological processes such as development, chromatin remodeling, stress responses and antiviral defense. ARGONAUTES (AGOs) are the effector proteins. They interact with other proteins, load sRNAs, and target and silence specific RNAs through sequence-specific interactions conferred by their guide sRNA.
Our group seeks to develop both new basic knowledge and biotechnological tools for crop improvement while addressing major gaps in the plant small RNA/AGO silencing field.
Our group main research interests are:
1. To better understand how silencing information is processed and expressed at the AGO complex level on a genome-wide scale, particularly in response to stress. AGO function is ultimately determined by its selective association with sRNA, target RNA and protein interactors, and this association changes in response to stresses. Extensive analyses by several laboratories have revealed the highly abundant, complex landscape of multiple sRNAs across plant genomes, and how these sRNAs associate with particular AGOs to exert their function. But, once AGO-sRNA complexes form, which are active to target mRNA and non-coding RNA? Are AGO sRNA-loading and/or mRNA targeting processes regulated by other protein bound to AGOs? The identification of the complete repertoire of AGO target RNAs and protein interactors is key to understand RNA-based silencing on a genome-wide scale. Also, to what extent are active complexes dynamic during physiologic responses to stress or environmental change?
2. To develop next-generation artificial sRNA-based RNAi (art-sRNAi) tools to control gene expression and induce antiviral resistance in plants. AGOs can be programmed with highly-specific, computationally-designed artificial sRNAs (art-sRNAs) to silence the desired gene(s) in gene function studies or for crop improvement. We have recently developed a new platform for high-throughput design and generation of art-sRNA constructs. We are using these tools to develop strategies for next-generation art-sRNAi. These strategies include fine-tuning the degree of art-sRNAi, inducing systemic silencing at the whole-plant level, controlling art-sRNAi in a spatio-temporal manner, increasing art-sRNA efficacy by targeting structurally accessible (TAM-including) sites, and developing GMO-free art-sRNAi approaches such as the exogenous application of art-sRNA precursors or their expression using viral vectors, as well as the possibility of using CRISPR to edit endogenous sRNA precursor genes to express art-sRNAs.
Adriana E. Cisneros, Purificación Lisón, Laura Campos, Joan Manel López-Tubau, Teresa Altabella, Albert Ferrer, José-Antonio Daròs, Alberto Carbonell*. Down-regulation of Tomato STEROL GLYCOSYLTRANSFERASE 1 Perturbs Plant Development and Facilitates Viroid Infection. Journal of Experimental Botany. In press.
María-Carmen Marqués, Javier Sánchez-Vicente, Raúl Ruiz, Roser Montagud-Martínez, Rosa Márquez-Costa, Gustavo Gómez, Alberto Carbonell, José-Antonio Daròs*, Guillermo Rodrigo* (2022). Diagnostics of plant viral infections with CRISPR-Cas12a and CRISPR-Cas13d. ACS Synthetic Biology 11 (7): 2384-2393.
Adriana E. Cisneros, Ainhoa de la Torre-Montaña, Alberto Carbonell* (2022). Systemic silencing of an endogenous plant gene by two classes of mobile 21-nucleotide artificial small RNAs. The Plant Journal 110 (4): 1166-1181.
Lucio López-Dolz, Maria Spada, José-Antonio Daròs and Alberto Carbonell* (2022). Fine-tune control of plant gene expression by synthetic trans-acting small interfering RNAs. In: Plant Gene Silencing: Methods and Protocols (Eds. Kirankumar Mysore and Muthappa Senthil-Kumar). Methods in Molecular Biology 2408: 227-242. Springer Protocols series, Humana Press, NY, USA. ISBN: 978-1-0716-1875-2.
Alberto Carbonell* (2022). RNAi tools for controlling viroid diseases. Virus Research 198729.
Vicente Pallás, Carmen Hernández, Jose Francisco Marcos, José-Antonio Daròs, Beatriz Navarro, José Antonio Navarro, Marcos de la Peña, Selma Gago-Zachert, María Eugenia Gas, Alberto Carbonell, Carmelo López, Ángel Emilio Martínez de Alba, Francesco Di Serio, Pedro Moreno (2022). In memoriam of Ricardo Flores: the career, achievements, and legacy of an inspirational plant virologist. Virus Research 198718.
Vicente Pallás Benet, Alberto Carbonell, Miguel Aranda, Blanca Landa del Castillo, Carlos López Herrera, Enrique Moriones Alonso, Juan A. Navas Cortés, Félix Ortego Alonso, Rafael Zas Arregui (2021). Plant health. Resistance to pests and diseases. In: Sustainable primary production (Eds. Enrique Olmos Aranda, Mónica Venegas Calerón), vol. 6: 85-105. CSIC Scientific Challenges: Towards 2030. Editorial CSIC. ISBN: 978-84-00-10748-2.
Adriana E. Cisneros, Ainhoa De la Torre-Montaña, Tamara Martín-García, Alberto Carbonell* (2021). Artificial small RNAs for functional genomics in plants. In: RNA-based technologies for functional genomics in plants (Eds. Guiliang Tang, Sachin Teotia, Xiaoqing Tang, Deepali Singh). Concepts and Strategies in Plant Sciences 16076: 1-29. Springer Nature. eBook ISBN: 978-3-030-64994-4.
Minglei Yang, Hugh Woolfenden, Yueying Zhang, Xiaofeng Fang, Qi Liu, Maria Louisa Vigh, Jitender Cheema, Xiaofei Yang, Matthew Norris, Sha Yu, Hang Zhang, Alberto Carbonell, Peter Brodersen, Jiawei Wang, Caroline Dean, Yiliang Ding* (2020). RNA structure-dependent activation of endonuclease RISC promotes miRNA cleavage in vivo. Nucleic Acids Research 48 (15): 8767-8781.
Adriana E. Cisneros and Alberto Carbonell* (2020). Art-sRNAi for enhanced antiviral resistance in plants. Encyclopedia (ISSN: ISSN 2309-3366): https://encyclopedia.pub/1870
Lucio López-Dolz, Maria Spada, José-Antonio Daròs, Alberto Carbonell* (2020). Fine-tune control of targeted RNAi efficacy by plant artificial small RNAs. Nucleic Acids Research 48 (11): 6234-6250.
Adriana E. Cisneros and Alberto Carbonell* (2020). Artificial Small RNA-Based Silencing Tools for Antiviral Resistance in Plants. Plants 9 (6): 669.
Pedro Serra, Alberto Carbonell, Beatriz Navarro, Selma Gago-Zachert, Shifang Li, Francesco Di Serio*, Ricardo Flores* (2020). Symptomatic plant viroid infections in phytopathogenic fungi: a request for a critical reassessment. Proceedings of the National Academy of Science 117 (19): 10126-10128.
Carbonell, A.*, Purificación Lisón and Daròs, J.A. (2019). Multi-targeting of viral RNAs with synthetic trans-acting small interfering RNAs enhances plant antiviral resistance. The Plant Journal 100: 720-737.
Cervera-Seco, L., Marqués, M.C., Sanz-Carbonell, A., Márquez-Molins, J., Carbonell, A., Daròs, J.A. and Gómez, G. (2019) Identification and characterization of a stress-responsive TAS3-derived tasiRNA in melon. Plant and Cell Physiology 60 (11): 2382-2393.
Carbonell, A.* and Daròs, J.A. (2019). Design, Synthesis, and Functional Analysis of Highly Specific Artificial Small RNAs With Antiviral Activity in Plants. In: Antiviral Resistance in Plants: Methods and Protocols (Eds. Kappei Kobayashi and Masamichi Nishiguchi). Methods in Molecular Biology 2028: 231-246.
Carbonell, A.* (2019). Secondary small interfering RNA-based silencing tools in plants: an update. Frontiers in Plant Science 10: 687.
Carbonell, A.* (2019). Design and high-throughput generation of artificial small RNA constructs for plants. In: Plant MicroRNAs: Methods and Protocols (Ed. Stephan de Folter). Methods in Molecular Biology 1932: 247-260.
Línea 1: Pequeños RNAs Artificiales: RNAi de Última Generación Para la Mejora de Cultivos (Art-sRNAi).
Entidad Financiadora: MICIU (AEI)/Cofinanciación FEDER. Referencia PID2021-122186OB-100. 01/09/2022-31/08/2025.
IP: Alberto Carbonell.
Línea 2: Complejos ARGONAUTA1 de Plantas: Identificación de sus Componentes Proteicos y de RNA, y Ajuste Fino del Silenciamiento Mediante su Programación por Pequeños RNAs Artificiales
Entidad Financiadora: MICIU (AEI)/Cofinanciación FEDER. Referencia RTI2018-095118-A-100. 01/01/2019-30/09/2022.
IP: Alberto Carbonell.
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Línea 2: RNA-based regulation of gene expression and antiviral resistance in plants
Entidad financiadora: MICIU (AEI)/Cofinanciación FEDER. Ayuda Ramón y Cajal. Referencia RYC-2017-21648. 16/01/2019-15/01/2024.
IP: Alberto Carbonell
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Línea 3: A sweet solution: novel antiviral siRNAs to help rescue the sugar beet industry
Entidad financiadora: European Research Council Proof of Concept, European Comission. Referencia PoC-2020-966855. 01/04/2020-30/09/2022.
IP: Yiliang Ding.
‘New Generation of Artificial MicroRNAs (PCT/US15/18529)’: patent pending. Filed on 04/03/2015.
‘Method for Modulating the Gene Silencing Degree Induced by Trans-acting Small Interfering RNAs (EP19382445.5): patent pending. Filed on 31/05/2019.
Estudio de complejos ARGONAUTA 1 en plantas: análisis de interactores y programación mediante pequeños RNAs artificiales para la regulación de la expresión génica y defensa antiviral
Doctorando: Adriana E. González Cisneros
