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
Differences in DNA binding specificity of floral homeotic protein complexes predict organ-specific target genesThe Plant Cell 29 (2017)8. - ISSN 1040-4651 - p. 1822 - 1835.
Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional ConservationThe Plant Cell 29 (2017)6. - ISSN 1040-4651 - p. 1278 - 1292.
SELEX-seq : A method to determine DNA binding specificities of plant transcription factorsIn: Plant gene regulatory networks / , Kaufmann, Kerstin, Mueller-Roeber, Bernd. - : Humana Press Inc. (Methods in Molecular Biology - Springer Protocols ) - ISBN 9781493971244 - p. 67 - 82.
Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plantsGenome Biology 18 (2017). - ISSN 1474-7596 - 12 p.
Splicing-related genes are alternatively spliced upon changes in ambient temperatures in plantsPLoS ONE 12 (2017)3. - ISSN 1932-6203
Cross-Family Transcription Factor Interactions : An Additional Layer of Gene RegulationTrends in Plant Science 22 (2017)1. - ISSN 1360-1385 - p. 66 - 80.
The Histone Deacetylase Inhibitor Trichostatin A Promotes Totipotency in Cultured Pollen: Plant Research International
Characterization of SOC1’s central role in flowering by the identification of its upstream and downstream regulators: Max Planck Institute for Developmental Biology
Temperature-dependent alternative splicing of FLM controls flowering in Arabidopsis thaliana: Max Planck Institute for Developmental Biology
Mysterie van de maisplant uit Alphen ontrafeldMysterie van de maisplant uit Alphen ontrafeld, De Gelderlander, 2016-06-13