My research group is interested in how developmental processes are controlled by transcription factors and chromatin modifications. We aim to unravel transcriptional networks underlying various processes such as flowering time regulation, floral organ development, fruit formation and embryogenesis. We apply various methods, such as ChIP-seq, RNA-seq, proteomics, microscopy, CRISPR/CAS9 technologies and in vitro assays, to build gene regulatory networks and study the role of genes and proteins involved in these developmental processes. We are using predominantly the model species Arabidopsis and tomato, but also aim to understand to what extent the networks and genes are conserved in other species, including crops.
A main question of our research is: How do Transcription factors work and what are their target genes? To answer this question we are studying the properties of transcription factors belonging to the MADS domain, AP2-like or TCP transcription factor families. Since these transcription factors form larger complexes we analyse the components of the complexes by immunoprecipitation followed by MS/MS (Smaczniak et al, 2012). Furthermore, we are interested in the target genes that they control. A standard technology in our lab is ChIP-seq to identify in vivo binding sites. In addition we use in vitro methods, such as EMSA and SELEX to understand the specificity of binding to certain DNA sequences. Our results show that the composition of the transcription factor complex determines in part the binding specificity to target DNA.
We aim to identify downstream target genes by ChIP-seq and RNA-seq approaches and decipher their role in various developmental processes, such as flowering, flower, fruit and embryo development by genetic and molecular studies. A more recent focus of the group are studies to understanding the role of promoter elements (CIS regulatory elements) and how they control transcription. For this purpose we make mutations in promoters using CRISPR/Cas9, aiming at modulating gene expression in vivo.
Group members and teams
Evolution transcription factor
Tomato Fruit development
ABA signalling promotes cell totipotency in the shoot apex of germinating embryosJournal of Experimental Botany 72 (2021)18. - ISSN 0022-0957 - p. 6418 - 6436.
Live Imaging of embryogenic structures in Brassica napus microspore embryo cultures highlights the developmental plasticity of induced totipotent cellsPlant Reproduction 33 (2020)3-4. - ISSN 2194-7953 - p. 143 - 158.
The rin, nor and Cnr spontaneous mutations inhibit tomato fruit ripening in additive and epistatic mannersPlant Science 294 (2020). - ISSN 0168-9452
Revisiting the Role of Master Regulators in Tomato RipeningTrends in Plant Science 25 (2020)3. - ISSN 1360-1385 - p. 291 - 301.
Seed maturation and post-harvest ripening negatively affect arabidopsis somatic embryogenesisPlant Cell, Tissue and Organ Culture: an international journal on in vitro culture of higher plants 139 (2019)1. - ISSN 0167-6857 - p. 17 - 27.
The Chromatin-Associated Protein PWO1 Interacts with Plant Nuclear Lamin-like Components to Regulate Nuclear SizeThe Plant Cell 31 (2019)5. - ISSN 1040-4651 - p. 1141 - 1154.
Comprehensive phenotyping reveals interactions and functions of Arabidopsis thaliana TCP genes in yield determinationThe Plant Journal 99 (2019)2. - ISSN 0960-7412 - p. 316 - 328.
Re-evaluation of transcription factor function in tomato fruit development and ripening with CRISPR/Cas9-mutagenesisScientific Reports 9 (2019)1. - ISSN 2045-2322
Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana: Wageningen University & Research
Arabidopsis thaliana ambient temperature responsive lncRNAs: Max Planck Institute for Plant Breeding Research