Gene Regulatory Networks in Plant Development

Group Structure

Group Leader: José Luis Riechmann (ICREA Research Professor)
Postdoctoral Researchers: Thilia Ferrier, Jian Jin (until December 2013), Tomás Matus (until December 2013),
PhD Students: Mariana Bustamante


Developmental processes in multicellular organisms are dependent on the cellular capacity for differential gene expression. That capacity (i.e., the developmental program of an organism) is hardwired and encoded in the genome. The global aim of our group is the characterization and understanding of gene regulatory networks underlying plant development, using a combination of genomic and genetic methods. We have used Arabidopsis flower development as a model and experimental system, and through the analysis of correlated transcription factor genome-wide binding (ChIP-Seq) and transcriptomic data, we characterize the role of several floral regulators. One of them is the floral meristem and organ identity gene APETALA1, which we characterized as a network hub and a developmental switch that orchestrates the initiation of flower development. We have followed those findings with a dynamic analysis of AP1 genome activities, to understand how the AP1 network functions in a developmental context over time. We are using similar approaches to characterize other transcriptional regulators involved in flower development, such as CAULIFOWER (CAL) and CUC1. CAL is a close AP1 paralog, with which AP1 is partially redundant, and it offers a tool to dissect at the network level the two different AP1 functions (meristem identity and organ development). In addition, these genome-wide analyses 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.

Research Projects

  • AP1 gene regulatory network
  • AP1 target genes
  • CAL gene regulatory network
  • CUC1 gene regulatory network
  • Novel sORFs involved in flower development
  • TOC1 gene regulatory network (collaborative work with Dr. Paloma Mas)

Selected Publications

Huang W., Perez-Garcia 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

Jiao, Y., Riechmann, J.L.
Genome-Wide Profiling of Uncapped mRNA
(2012) In: Plant Signaling Networks, Z.-Y. Wang and Z. Yang (eds.), Methods in Molecular Biology, Volume 876, 207-216. Humana Press, Springer, New York.

Hassibi, A., Vikalo, H., Riechmann, J.L., Hassibi, B.
FRET-based real-time DNA microarrays.
(2012) In: Functional Genomics – part 3, M. Kaufmann and C. Klinger (eds.), Methods in Molecular Biology, Volume 815, 147-159. Humana Press, Springer, New York.