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
Arabidopsis thaliana ambient temperature responsive lncRNAs: Max Planck Institute for Plant Breeding Research
PISTILLATA paralogs in Tarenaya hassleriana have diverged in interaction specificityBMC Plant Biology 18 (2018)1. - ISSN 1471-2229
Arabidopsis thaliana ambient temperature responsive lncRNAsBMC Plant Biology 18 (2018)1. - ISSN 1471-2229
Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thalianaBMC Plant Biology 18 (2018)1. - ISSN 1471-2229
A molecular network for functional versatility of HECATE transcription factorsThe Plant Journal 95 (2018)1. - ISSN 0960-7412 - p. 57 - 70.
The Arabidopsis transcription factor TCP5 during petal and inflorescence development: Wageningen University and Research
Novel functions of the Arabidopsis transcription factor TCP5 in petal development and ethylene biosynthesisThe Plant Journal 94 (2018)5. - ISSN 0960-7412 - p. 867 - 879.
Genetic control of meristem arrest and life span in Arabidopsis by a FRUITFULL-APETALA2 pathwayNature Communications 9 (2018)1. - ISSN 2041-1723
A seed treatment to prevent shoot apical meristem arrest in Brassica oleraceaScientia Horticulturae 228 (2018). - ISSN 0304-4238 - p. 76 - 80.
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.