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
Identification of in planta protein–protein interactions using IP-MSIn: Plant Chromatin Dynamics / , Bemer, M., Baroux, C.. - : Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781493973170 - p. 315 - 329.
Profiling nucleosome occupancy by MNase-seq : Experimental protocol and computational analysisIn: Plant Chromatin Dynamics / , Bemer, M., Baroux, C.. - : Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781493973170 - p. 167 - 181.
Divergent regulation of Arabidopsis SAUR genes: a focus on the SAUR10-clade: Wageningen University & Research
Inhibition of bolting and flowering of a beta vulgaris plantOctrooinummer: WO2017072304, gepubliceerd: 2017-05-04.
Divergent regulation of Arabidopsis SAUR genes : A focus on the SAUR10-cladeBMC Plant Biology 17 (2017). - ISSN 1471-2229
A cautionary note on the use of chromosome conformation capture in plantsPlant Methods 13 (2017)1. - ISSN 1746-4811
Targets of FRUITFULL in the pistil/silique [ChIP-Seq]: Wageningen University
Expression profile of Arabidopsis pistil/silique upon induction of FRUITFULL: Wageningen University
FRUITFULL controls SAUR10 expression and regulates Arabidopsis growth and architectureJournal of Experimental Botany 68 (2017)13. - ISSN 0022-0957 - p. 3391 - 3403.
The BABY BOOM transcription factor activates the LEC1-ABI3-FUS3-LEC2 network to induce somatic embryogenesisPlant Physiology 175 (2017)2. - ISSN 0032-0889 - p. 848 - 857.