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Epigenetic regulation of plant immunity

Primary Supervisor: Professor Vardis Ntoukakis, School of Life Sciences

Secondary supervisor: Professor Miriam Gifford

PhD project title: Epigenetic regulation of plant immunity

University of Registration: University of Warwick

Project outline:

Activation of plant immunity has to be finely balanced with other vital biological processes such as development and growth.  A major part of plant immune responses is reprogramming of gene expression. During infection, plants are faced with the challenge of quickly changing their state of gene transcription by prioritizing defence responses over growth-related cellular functions. In all eukaryotic organisms the genomic DNA is packed into chromatin providing at the same time a barrier for transcription and an opportunity to regulate rapid changes in gene expression. A major mechanism controlling changes in chromatin structure and subsequently the partial/differential expression of the genome is localized chromatin remodelling.

Our laboratory has recently demonstrated that chromatin remodelling is a major mechanism controlling plant immunity1,2,3.

The aim of the two PhD project offered is to investigate the role of chromatin remodelling and epigenetics in the interplay between immunity and growth.

  • The first PhD project will investigate the role of histone acetyltransferases and deacetylases in the interplay between immunity and growth.

Histone-modifying enzymes add or remove covalent histone modifications that alter the accessibility of DNA to transcription factors, mediating the dynamic transition between expressed and repressed genomic regions. Histone acetylation is mediated by histone acetyltransferases (HATs) and deacetylases (HDACs), which deposit and remove acetyl groups from histones. The addition of acetyl groups on the N-terminus tails of histones reduce the affinity between histones and DNA, allowing the recruitment of the transcriptional machinery. Our laboratory has recently show that HATs regulate leaf immunity1 and inheritable resistance against root pathogens2. The aim of this project is to elucidate how HATs and HDACs regulate plant immunity against leaf and root pathogens.

  • The second PhD project will focus on the role of ATP-dependent chromatin remodelling complexes in regulating plant immunity and growth.

ATP-dependent chromatin remodeling complexes regulate transcription through their ability to evict, slide or reposition nucleosomes around DNA. Our laboratory has recently demonstrated that multiple ATP-dependent chromatin remodeling complexes regulate immunity3. The aim of this project is to elucidate how ATP-dependent chromatin remodeling complexes regulate plant immunity.

The successful students will use cutting edge techniques including RNA-seq, ChIP-seq, MNase-seq and ATAC-seq together with statistical analysis and modelling to gain insight into the interplay between immunity and growth. After the initial characterisation using Arabidopsis thaliana plants, we will expand our investigation to tomato and brassica plants using CRISPR/Cas9 gene editing.

References:

  1. Kim S., Piquerez S.J.M., Ramirez-Prado J.S., Mastorakis E., Veluchamy A., Latrasse D., Manza-Mianza D., Brik-Chaouche R., Huang Y, Rodriguez-Granados N.Y., Concia L., Blein T., Citerne S., Bendahmane A., Bergounioux C., Crespi M., Mahfouz M.M., Raynaud C., Hirt H., Benhamed M. Ntoukakis V. (2020) GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5' and 3' ends of its target genes. Nucleic Acids Res., 48, (11), 5953-5966.
  2. Gkizi D., González A.G., Pardal A. J., Piquerez S.J.M., Sergaki C., Tjamos S.E., Ntoukakis V. (2021) The bacterial biocontrol agent Paenibacillus alvei K165 confers inherited resistance against Verticillium dahliae. J. Exp. Bot. 72 (12), 4565-4576
  1. Pardal A. J., Piquerez S.J.M., Dominguez-Ferreras A., Frungillo L., Mastorakis E., Reilly E., Latrasse D., Concia L., Gimenez-Ibanez S., Spoel S.H., Benhamed M., Ntoukakis V. (2020) Immunity onset alters plant chromatin and utilizes EDA16 to regulate oxidative homeostasis. PLos Pathogens, 17 (5), e1009572

BBSRC Strategic Research Priority: Sustainable Agriculture and Food: Plant and Crop Science & Understanding the Rules of Life: Plant Science

    Techniques that will be undertaken during the project:

    The successful students will use cutting edge techniques including RNA-seq, ChIP-seq, MNase-seq and ATAC-seq together with statistical analysis and modelling to gain insight into the interplay between immunity and growth. After the initial characterisation using Arabidopsis thaliana plants, we will expand our investigation to tomato and brassica plants using CRISPR/Cas9 gene editing.

    Contact: Professor Vardis Ntoukakis, University of Warwick