Gene regulatory networks in plant development

Group Leaders
José Luis Riechmann
ICREA Research Professor
Group Members
Gene Regulatory Networks in Plant Development group

Postdoctoral Researchers

Undergrad or Master Students


Developmental processes in multicellular organisms are dependent on the cellular capacity for differential gene expression. The global aim of our group is the characterization and understanding of gene regulatory networks underlying plant development, using a combination of genomic, proteomic and genetic methods.

We use Arabidopsis flower development as our model and primary experimental system, as the onset of flower formation and the process of flower development are excellent paradigms for developmental studies in plants. Through the analysis of transcription factor genome-wide binding and transcriptomic data, we characterized the role of the floral meristem and organ identity gene APETALA1 as a network hub and a developmental switch that orchestrates the initiation of flower development. We are using similar approaches to characterize other transcriptional regulators involved in flower development. 

These and other studies are providing a global, dynamic view of the floral developmental process. However, this view is primarily based on measuring gene expression at the transcriptome level. Thus, an additional current area of activity in the group is to combine genomic, proteomic, and peptidomic technologies to study these processes, and to determine how the transcriptome and the proteome are correlated throughout flower development in Arabidopsis.

These genome-wide analyses also identify a large number of transcription factor target genes, most of which are uncharacterized, but that can now be studied using the extensive Arabidopsis genetic and molecular toolkit.

Selected Publications

Álvarez-Urdiola, R., Borràs, E., Valverde, F., Matus, J. T., Sabidó, E., and Riechmann, J.L.
Peptidomics methods applied to the study of flower development
(2023) Methods in Molecular Biology, vol. 2686, pp. 509-536.

Álvarez-Urdiola, R., Matus, J. T., and Riechmann, J.L.
Multi-omics methods applied to flower development
(2023) Methods in Molecular Biology, vol. 2686, pp. 495-508.

Fàbregas, N., Lozano-Elena, F., Blasco-Escámez, D., Tohge, T., Martínez-Andújar, C., Albacete, A., Osorio, S., Bustamante, M., Riechmann, J.L., Nomura, T., Yokota, T., Conesa, A., Alfocea, F.P., Fernie, A.R., Caño-Delgado, A.I.
Overexpression of the vascular brassinosteroid receptor BRL3 confers drought resistance without penalizing plant growth
(2018) Nature Communications, vol. 9 (1), Art. number 4680

Bustamante, M., Matus, J.T., Riechmann, J.L.
Genome-wide analyses for dissecting gene regulatory networks in the shoot apical meristem
(2016) Journal of Experimental Botany, vol. 67 (6), pp. 1639-1648

Pajoro, A., Madrigal, P., Muiño, J.M., Matus, J.T., Jin, J., Mecchia, M.A., Debernardi, J.M., Palatnik, J.F., Balazadeh, S., Arif, M., Ó'Maoiléidigh, D.S., Wellmer, F., Krajewski, P., Riechmann, J.-L., Angenent, G.C., Kaufmann, K.
Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
(2014) Genome Biology, vol. 15 (3), Art. number R41

Wellmer, F., Bowman, J.L., Davies, B., Ferrándiz, C., Fletcher, J.C., Franks, R.G., Graciet, E., Gregis, V., Ito, T., Jack, T.P., Jiao, Y., Kater, M.M., Ma, H., Meyerowitz, E.M., Prunet, N., Riechmann, J.L.
Flower development: Open questions and future directions
(2014) Methods in Molecular Biology, vol. 1110, pp. 103-124

Wellmer, F., Graciet, E., Riechmann, J.L.
Specification of floral organs in Arabidopsis
(2014) Journal of Experimental Botany, vol. 65 (1), pp. 1-9

Huang, W., Pérez-García, P., Pokhilko, A., Millar, A.J., Antoshechkin, I., Riechmann, J.L., Mas, P.
Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator
(2012) Science, vol. 335 (6077), pp. 75-79

Ferrier, T., Matus, J.T., Jin, J., Riechmann, J.L.
Arabidopsis paves the way: Genomic and network analyses in crops
(2011) Current Opinion in Biotechnology, vol. 22 (2), pp. 260-270

Wellmer, F., Riechmann, J.L.
Gene networks controlling the initiation of flower development
(2010) Trends in Genetics, vol. 26 (12), pp. 519-527

Kaufmann, K., Wellmer, F., Muiñ, J.M., Ferner, T., Wuest, S.E., Kumar, V., Serrano-Mislata, A., Madueño, F., Kraiewski, P., Meyerowitz, E.M., Angenent, G.C., Riechmann, J.L.
Orchestration of floral initiation by APETALA1
(2010) Science, vol. 328 (5974), pp. 85-89