Our research focuses on how epigenetic mechanisms regulate key developmental processes and genome organization in plants. To address these questions, we employ molecular genetics, biochemical analyses, and advanced epigenomics techniques. We focus on developmental processes that directly impact crop productivity, especially flowering time — a critical factor with major implications for future agriculture. To this end, our work spans both the model plant Arabidopsis thaliana and agriculturally important Brassica species (Brassica rapa and Brassica napus). By bridging fundamental and applied research in plant epigenetics, our work not only advances our understanding of chromatin-based regulation but also contributes to the development of tools for improving crop resilience and adaptability to changing environmental conditions.
 
 
Figure 1. Translational research program from Arabidopsis to Brassica crops. We translate research from Arabidopsis thaliana to Brassica crop species, combining molecular genetic, biochemical, and state-of-the-art genomics approaches to unravel the epigenetic basis of key agronomic traits.

 
RESEARCH LINES

Role of histone demethylases on plant development
We investigate the dynamic epigenetic regulation mediated by H3K27me3, a repressive histone modification conserved across both plants and animals. H3K27me3 critically controls transcriptional repression necessary for proper plant development and effective environmental responses. This mark is established by the Polycomb Repressive Complex 2 (PRC2), a specialized histone methyltransferase complex, and is precisely removed by Jumonji-C domain-containing histone demethylases.
 
 
Figure 2. Epigenetic Switching via H3K27me3. The repressive epigenetic mark H3K27me3 is deposited by the PRC2 complex, leading to gene silencing through chromatin compaction. H3K27 demethylases counteract this repression by removing the methyl groups, thereby activating gene expression. This dynamic equilibrium controls critical developmental processes in plants.

H3K27me histone demethylases function as molecular switches, removing repressive marks to activate developmental gene networks at precise times and locations. To unveil the function of these histone demethylases in plant development, we pursue two interconnected research directions. First, we investigate how histone demethylases regulate key developmental processes, including flowering time, flower development, and fruit formation. We recently found that H3K27me3 histone demethylases exhibit both conserved and distinct roles in regulating flowering time between Arabidopsis and Brassica crops.
 
Figure 3. Conserved and divergent roles of H3K27me3 demethylases regulating flowering time in A. thaliana and B. rapa. (A) Schematic model illustrating the mechanism by how the histone demethylases ELF6 and REF6 regulating flowering time in Arabidopsis and B. rapa. (B) Phenotype of B. rapa braA.ref6 mutants, showing a characteristic delayed flowering time.

Second, we study how histone demethylases enable plants to modify their developmental programs in response to environmental cues, particularly light and temperature changes. We examine how these signals are translated into epigenetic modifications that reprogram gene expression and developmental outcomes. Our findings demonstrate that histone demethylases function as molecular integrators, allowing plants to dynamically adjust their epigenetic landscapes in response to environmental signals. This research reveals how plants coordinate internal developmental programs with external environmental information, providing insights into plant adaptation strategies and developmental plasticity mechanisms.
 
 
Figure 4. Arabidopsis ELF6 and JMJ13 regulate flowering time response to ambient temperature. Model illustrating that the expression of genes encoding floral regulators is precisely regulated by Polycomb Repressive Complex 2 (PRC2) and H3K27me3 histone demethylases. This epigenetic balance ensures appropriate transcriptional levels, allowing the plant to respond accurately to changes in ambient temperature.

Effect of fluctuating temperatures on chromatin silencing
Plant development occurs at different pace in diverse ambient temperatures but also under constant versus fluctuating temperature conditions. Within the framework of the CBGP-CEPLAS International Collaborative Scientific Program, we are investigating how changes in chromatin states are associated with both short-term and long-term responses to fluctuating ambient temperatures. This research is crucial for gaining a better understanding of how plants adapt to temperature changes, which, in turn, is essential for developing crops that are resilient to the challenges of climate change.
 
 
Figure 5. Nuclear localization of chromatin remodeling proteins visualized by confocal microscopy in Arabidopsis root cells. We examine chromatin dynamics under changing environmental conditions by tracking the nuclear localization patterns of key chromatin remodeling proteins and their associated epigenetic marks.

Deciphering the plant epigenome
We leverage state-of-the-art genomic and epigenomic technologies to precisely dissect the function of critical epigenetic modifications within the Arabidopsis and Brassica genomes. In past years, our research has significantly advanced Brassica epigenomics. Key achievements of Brassica research include: generating the first H3K27me3 genome-wide profile creating a foundational resource; and pioneering studies of epigenetic modifier mutants.

We recently started a collaborative research program with researchers form the Institute of Vegetables and Flowers (CAAS, China) to advance the understanding of Brassica genome complexity. We are performing pan-genomic structural variation analysis and mapping the three-dimensional organization of the genome. Through this multi-layered genome analysis, we aim to uncover fundamental mechanisms that shape genome evolution and structural diversity in plants.
 
 
Figure 6: Integrated epigenomic and transcriptomic Analyses. (A) ChIP-seq metagene plot showing that H3K27me3 enrichment is strongly correlated with transcriptionally repressed genes. (B) Transcriptomic comparison of wild-type and mutant lines across developmental stages reveals clusters of differentially expressed genes.

Co-transcriptional regulation in plants
This line of research is led by Eduardo Mateo-Bonmatí and focus on understanding how transcription and co-transcriptional processes interact to shape the chromatin environment. To explore these mechanisms, we use the well-characterized A. thaliana FLOWERING LOCUS C (FLC), a paradigm gene for studying epigenetic and chromatin-mediated regulatory mechanisms.

PROSPECTIVE STUDENTS

We are a dynamic and collaborative research team exploring the molecular and epigenetic mechanisms that shape plant development. Scientists at different career stages work side by side, united by curiosity and a shared commitment to discovery. Mentoring young researchers is a core part of what we do, providing hands-on training that builds both technical expertise and scientific confidence.

Our lab is a place to grow — scientifically and personally. Students are encouraged to think critically, communicate effectively, and pursue innovative ideas that advance plant science. We aim to empower the next generation of scientists to lead impactful research careers in academia, industry, and beyond.

 

 

 

Crevillen Lomas, Pedro - Researcher CSIC

Jarillo Naranjo, Fátima - Technician

Luna Morales, Ana María - PhD Student

Márquez Pazanin, Cristian - Student

Mateo Bonmatí, Eduardo - Ramón y Cajal fellow

Olmo Montoro, Iván del - Postdoctoral Fellow

Pérez García, Carolina - TFM Student

Ruiz Gómez, Pablo - TFG Student

Sempere González, Andrea - PhD Student

Valladares Aguirre, Sara - PhD Student

    • COOPB25029. PAN-GENOME ARCHITECTURE AND EPIGENETIC REGULATION IN BRASSICAS. 2026-2027. Programa I-COOP de cooperación científica para el desarrollo 2025, CSIC. PI: Pedro Crevillén

 

    • PID2024-156598NB-I00. EPIGENETIC REGULATION OF FLOWERING LOCUS M: A MECHANISM TO UNDERSTAND HOW CLIMATE CHANGE ALTERS FLOWERING TIME (EPIFLOWERMECH). 2025-2028. Proyectos Generación de Conocimiento 2024, Agencia Estatal de Investigación. PI: Pedro Crevillén

 

    • PID2023-147737NA-I00. UNDERSTANDING HOW CPSF PHOSPHATASE MODULE INFLUENCES CO-TRANSCRIPTIONAL REGULATION IN PLANTS. 2024-2027. Ministerio de Ciencia, Innovación y Universidades/Agencia Estatal de Investigación (MICIU/AEI), Spain. PI: Eduardo Mateo-Bonmatí

 

    • PID2021-122241OB-I00. EPIGENETIC REGULATION OF FRUIT DEVELOPMENT AND SEED YIELD IN BRASSICA OILSEED CROPS. 01/09/2025-30/08/2027. Ministerio de Ciencia, Innovación y Universidades/Agencia Estatal de Investigación (MICIU/AEI), Spain and FEDER, EU. PI: Pedro Crevillén

 

    • RYC2021‐030895‐I. Ayuda Ramón y Cajal. 2023-2027. Ministerio de Ciencia, Innovación y Universidades/Agencia Estatal de Investigación (MICIU/AEI), Spain and European Union NextGenerationEU/PRTR.  PI: Eduardo Mateo-Bonmatí

 

    • CEX2020-000999-S. Effect of fluctuating temperatures on chromatin silencing and its impact on growth in Brassica crops. 01/09/2025-30/08/2027. Ministerio de Ciencia, Innovación y Universidades/Agencia Estatal de Investigación (MICIU/AEI), Spain and Severo Ochoa Excellence program.  PI: Pedro Crevillén

Barrero-Gil, J., Mouriz, A., Piqueras, R., Tian, Y., López, J.A., Vázquez, J., Crevillén, P., Jarillo, J.A.✉, Piñeiro, M.✉ 2025. Arabidopsis INHIBITOR OF GROWTH 2 promotes flowering by regulating NuA4-dependent H4 acetylation levels at FT and SOC1. Plant Physiology. DOI: 10.1093/plphys/kiaf511

Poza-Viejo, L., Payá-Milans, M., Wilkinson, M.D., Piñeiro, M., Jarillo, J.A., Crevillén, P. 2024. Brassica rapa CURLY LEAF is a major H3K27 methyltransferase regulating flowering time. Planta 260, 27. DOI: 10.1007/s00425-024-04454-7

Mateo-Bonmatí, E., Montez, M., Maple, R., Fiedler, M., Fang, X., Saalbach, G., Passmore, L.A., Dean, C. 2024. A CPF-like phosphatase module links transcription termination to chromatin silencing. Molecular Cell. DOI: 10.1016/j.molcel.2024.05.016

 

Menon, G., Mateo-Bonmati, E., Reeck, S., Maple, R., Wu, Z., Ietswaart, R., Dean, C., Howard, M. 2024. Proximal termination generates a transcriptional state that determines the rate of establishment of Polycomb silencing. Molecular Cell. DOI: 10.1016/j.molcel.2024.05.014

Nielsen, M., Menon, G., Zhao, Y., Mateo-Bonmati, E., Wolff, P., Zhou, S., Howard, M., Dean, C. 2024. COOLAIR and PRC2 function in parallel to silence FLC during vernalization. Proceedings of the National Academy of Sciences 121, e2311474121. DOI: 10.1073/pnas.2311474121

Poza-Viejo, L., Payá-Milans, M., Martín-Uriz, P.S., Castro-Labrador, L., Lara-Astiaso, D., Wilkinson, M.D., Piñeiro, M., Jarillo, J.A., Crevillén, P. 2022. Conserved and distinct roles of H3K27me3 demethylases regulating flowering time in Brassica rapa. Plant, Cell & Environment n/a. DOI: 10.1111/pce.14258

Shukla, A., Pagán, I., Crevillén, P., Alonso-Blanco, C., García-Arenal, F. 2021. A role of flowering genes in the tolerance of Arabidopsis thaliana to cucumber mosaic virus. Molecular Plant Pathology. DOI: 10.1111/mpp.13151

Crevillén, P. 2020. Histone Demethylases as Counterbalance to H3K27me3 Silencing in Plants. iScience 23, 101715. DOI: 10.1016/j.isci.2020.101715

Payá-Milans, M., Poza-Viejo, L., Martín-Uriz, P.S., Lara-Astiaso, D., Wilkinson, M.D., Crevillén, P. 2019. Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa. GigaScience 8. DOI: 10.1093/gigascience/giz147

del Olmo, I., Poza‐Viejo, L., Piñeiro, M., Jarillo, J.A., Crevillén, P. 2019. High ambient temperature leads to reduced FT expression and delayed flowering in Brassica rapa via a mechanism associated with H2A.Z dynamics. The Plant Journal. DOI: 10.1111/tpj.14446

Crevillén, P., Gómez‐Zambrano, Á., López, J.A., Vázquez, J., Piñeiro, M., Jarillo, J.A. 2019. Arabidopsis YAF9 histone readers modulate flowering time through NuA4-complex-dependent H4 and H2A.Z histone acetylation at FLC chromatin. New Phytologist. DOI: 10.1111/nph.15737

Huertas, R., Catalá, R., Jimenez-Gomez, J., Castellano, M.M., Crevillén, P., Piñeiro, M., Jarillo, J.A., Salinas, J. 2019. Arabidopsis SME1 regulates plant development and response to abiotic stress by determining spliceosome activity specificity. The Plant Cell tpc.00689.2018. DOI: 10.1105/tpc.18.00689