Research interest: 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.
The PIs in the group are:
Group members (from left to right):
- prof. dr. Gerco Angenent, group leader
- dr. Kim Boutilier, senior researcher
- dr. Ruud de Maagd, senior researcher
- prof. dr. Richard Immink, senior researcher
- dr. Steven Groot, senior researcher
- dr. Marian Bemer, researcher
- dr. Martijn Fiers, researcher
- dr. Amalia Diaz Granados, post-doc
- dr.Amit Kumar, post-doc
- dr. Baojian Chen, post-doc
- dr. Rufang Wang, post-doc
- Marco Busscher, technician
- Jan Kodde, technician
- Tjitske Riksen, technician
- Mieke Weemen, technician
- Froukje van der Wal, technician
- Jacqueline Busscher-Lange, technician
- Michiel Lammers, technician
- Chris Roelofsen, technician
- Vera Veltkamp, PhD student (with Ruud de Maagd)
- Lena Maas, PhD student (with Kim Boutilier)
- Ellen Slaman, PhD student (with Ruud de Maagd)
- Annemarie Castricum, PhD student (with Richard Immink, Marian Bemer)
- Charlotte Siemons, PhD student (with Kim Boutilier)
- Xiaobing Jiang (with Marian Bemer)
- Francesca Bellinazzo, PhD student (with Richard Immink)
- Suze Blom, PhD student (with Richard Immink)
- Judit Nadal, PhD student (with Richard Immink)
- Iris Zahn, PhD student (with Marian Bemer)
- Gül Hatinoglu, PhD student (with Ruud de Maagd and Richard Immink)
- Kai Thoris, PhD student (with Marian Bemer)
- Victor Aprilyanto, PhD student (with Ruud de Maagd)
The following PhD students from our group successfully defended their thesis:
Doctorate degree Rufan Wang. February 18, 2020, Wageningen University.
'Genetic and epigenetic regulation of tomato fruit ripening'
Doctorate degree Sam van Es
"Sculpting a plant: TCP transcription factors as key regulators of plant growth and development.
"Wageningen, 18 September 2018
Doctorate degree for Suraj Jamge
"MADS efloral integrators: Insights into molecular mechanisms of MADS domain proteins in the floral transition."
Wageningen February 9, 2018
Doctorate degree for Suzanne de Bruijn
"MADS evolution: Insights into the evolutionary changes in transcription factors and their binding sites
"Wageningen, November 20, 2017
Doctorate degree for Hilda van Mourik
"MADS specificity: Unravelling the dual function of the MADS domain protein FRUITFULL"
Wageningen November 10, 2017