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Single-cell analysis of stress memory in plants

Principal Supervisor: Professor Jose Gutierrez-Marcos, School of Life Sciences

Co-supervisor: Dr Andre Pires da Silva, School of Life Sciences

PhD project title: Single-cell analysis of stress memory in plants

University of Registration: University of Warwick

Project outline:

Plants are sessile organisms that are known for their adaptive plasticity to the changing environment. Environmental changes cannot only influence gene expression patterns but also affect the stability of the genome. Both of these responses seem to involve epigenetic mechanisms. Recent data suggest that environmental signals, in addition to the direct influence on plant growth, can also cause phenotypic changes that can be transmitted to the progeny, sometimes remaining stable for several generations. In this respect, the formation of environmental epialleles and their maintenance represents an important, yet unexplored, source of variation and adaptive power that can contribute to rapid evolution and more importantly to the improvement of crop plants.

The aim of this project is to investigate (i) how environmental signals are able to modify the epigenome of meristematic cells to facilitate their somatic transmission and (ii) how these environmental imprints are maintained across generations after sexual propagation. Using Arabidopsis as a plant model system, the student will investigate, the inheritance of epigenetic modifications upon environmental stress, use known epigenetic mutants to obtain clues about the genetic pathway(s) implicated and the targeted engineering of identified genomic regions to reveal their function. It is expected that the student will be able to test the different by combining computational and laboratory analyses.

Key Skills involved:

The student will gain skills in single-cell epigenomic analysis (bisulphite sequencing, chromatin mapping and mRNA/small RNA profiling). The student will be able to analyse next-generation sequencing (NGS) data to generate hypothesis that will be tested in the laboratory using established genome and epigenome targeting methods. In addition, the student is expected to obtain basic training on computational and statistical tools for analysis of genome-wide data.

The student will work on a cellular model for the intregration and transmission of stress memory using state-of-the-art microscopy techniques and computational analyses.

Key References:

  1. Wibowo A., et al., Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and restricted in the male germline by DNA glycosylase activity (2016). eLife 5:e13546
  2. Becker, C., et al., Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature (2011) 480: 245-9.
  3. Krishnaswami, S.R. et al., Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons (2016) Nature Protocols 11:499-524

BBSRC Strategic Research Priority: Sustainable Agriculture and Food: Plant and Crop Science

Techniques that will be undertaken during the project:

The student will use a wide range of molecular, histological and computational techniques including: Genomic and Epigenomic analysis using Next Generation Sequencing data and customised computational analysis. In addition, he/she will use advanced microscopy and computational image analysis.

Contact: Dr Jose Gutierrez Marcos, University of Warwick