Histone Acetylation and in vitro Embryogenesis - Molecular Biology

Haploid male (micropores/pollen) or female (egg cells) reproductive cells can be induced to regenerate in vitro into a complete plant via embryogenesis. How these cells initiate embryogenic growth in the absence of fertilization in response to inducing signals is poorly understood.

Description

We have shown that chemical inhibitors of histone deacetylases (HDACi), which epigenetically control gene expression through histone deacetylation, are potent inducers of in vitro haploid embryo development from microsores/pollen (Li et al., 2015). In this project we will investigate the mode of action of these compounds by 1) analysing changes in histone acetylation and other chromatin marks that promote haploid embryogenesis and 2) identifying and characterizing the specific proteins targeted by these epidrugs. Previously we have used RNA sequencing approach to identify the differentially expressed genes from embryogenic culture upon HDACi treatment. Presently we are performing ATAC seq and ChIP seq analysis to investigate the impact of epigenetic modifications that promote haploid embryogenesis. Additionally, we are generating and characterizing candidate histone deacetlayse and acetyltransferase mutants to investigate their role in haploid embryogenesis.

histone_acetylation_bew.jpg

Used skills

  • RNA -sequencing
  • ChIP-Sequencing
  • ATAC sequencing
  • FACS
  • CRISPR-Cas9 mutagenesis (in silico sgRNA design, plasmid construction)
  • Protein-DNA interactions (yeast 1 hybrid analysis)
  • Genetic analysis of Brassica napus and arabidopsis mutants
  • Gene expression analysis (RNA isolation, qRT-PCR)
  • Chemical screening of epigrugs
  • Microspore culture

Requirements

  • Good theoretical and practical basis in (plant) molecular biology

Student projects

  • Please contact me if you are interested in working on next-generation sequencing techniques , HDAC and HAT mutant characterization or chemical screens to study epigenetic mechanisms involved in haploid embryogenesis.