Ph.D. Topics

1. Investigating pre-mRNA alternative splicing during the embryonic thermoresponse in Arabidopsis thaliana

Supervisor: Helene Robert Boisivon, Ph.D.


Transcript variants generated by alternative splicing (AS) of a precursor mRNA transcript expand the cellular protein catalog for the plant response to various stresses without the requirement of de novo transcription. AS is a molecular strategy taken by plants under temperature stress to limit the adverse effects of high temperatures and to adjust their growth and physiology during the stress period. Spliced variants may be targeted for degradation by non-sense mediated decay (NMD) or encode alternative proteins to feedback on the stress response. Heat Shock Proteins (HSP) and Heat Shock Factors (HSF) are among the targets of temperature-induced AS. Our lab investigates how high temperatures affect embryo morphogenesis and seed development. We identified that AS regulators are upregulated in seeds of plants grown at high temperatures. The project will investigate the implications of AS in the morphogenic alterations of Arabidopsis embryos when developing at high temperatures. The proposed experimental approaches include profiling of AS events in high-temperature seeds by nanopore RNA sequencing. Specific candidates whose transcripts are targeted by AS at high temperatures, and known for their involvement in embryo morphogenesis, will be functionally characterized: expression analysis (microscopy), phenotyping (genetics), ectopic expression (cloning, generation of transgenics), etc.

The Ph.D. topic is part of a collaborative project with the research team led by Dr. Said Hafidh in the lab of Prof. Honys at the Institute of Experimental Botany in Prague.

Requirements on candidates:

The candidate will have notions of bioinformatics. The candidate has experience in molecular biology (cloning, RT-qPCR), expression analysis (microscopy), and masters the notions of plant genetics and epigenetics.

Recommended literature:

  1. John, S., Olas, J. J. & Roeber, B. M. Regulation of alternative splicing in response to temperature variation in plants. J Exp Bot erab232 (2021) doi:10.1093/jxb/erab232.
  2. Kulichová, K. et al. PRP8A and PRP8B spliceosome subunits act coordinately to control pollen tube attraction in Arabidopsis thaliana. Development (Cambridge, England) 147, dev186742 (2020).
  3. Mácová, K. et al. Effects of long-term high-temperature stress on reproductive growth and seed development in development in Brassica napus. Biorxiv 2021.03.11.434971 (2021) doi:10.1101/2021.03.11.434971.
  4. Robert, H. S. et al. Local auxin sources orient the apical-basal axis in Arabidopsis embryos. Current Biology 23, 2506–2512 (2013).
  5. Verma, S., Attuluri, V. P. S. & Robert, H. S. An Essential Function for Auxin in Embryo Development. Csh Perspect Biol 13, a039966 (2021).

Keywords:      Arabidopsis thaliana, embryogenesis, high temperatures, alternative splicing