International PhD Fellowships in RNA Biotechnology

Plants have an amazing ability to deal with changing environments through molecular mechanisms that facilitate adaptation. We are looking for an exceptionally motivated Ph. D. student to elucidate temperature-sensing properties of short promoter-proximal RNAs (sppRNAs) that are connected to temperature responsive plant gene expression. sppRNAs are transcript isoforms resulting from partial RNA polymerase II (RNAPII) transcription of plant genes, linked to promoter-proximal stalling of RNAPII during gene expression. For detailed information on sppRNAs and project background please see: https://www.nature.com/articles/s41467-020-16390-7. The project operates at the interface between the research areas of: epigenetics, RNA biology, RNAPII transcription and genomics. You will be based in the laboratory of Sebastian Marquardt, University of Copenhagen, Denmark, and visit the laboratory of Zachary Lippman, Cold Spring Harbor Laboratory, USA, to perform the parts of your project, particularly elements in tomato.
You will characterize temperature-sensitive characteristics of plant gene expression in Arabidopsis and tomato. A key element of your project will be the characterization of molecular mechanisms triggering sppRNA formation during plant gene expression during changing temperature with a focus on cold. This Ph.D. project involves design, execution and analysis of transcriptomics and epigenomics Next-Generation Sequencing (NGS) data. Expertise and enthusiasm to analyze NGS data characterize candidates that match the profile for this position. You will examine sppRNAs in tomato, which will involve targeted genetic engineering of tomato using CRISPR/Cas9. Tomato is sensitive to cold temperatures, which affects yield. Your project will test the hypothesis that part of the cold sensitivity of tomato may be rooted in differences of sppRNA-based cold sensing compared to plants that are more resistant to cold (i.e. Arabidopsis).  This project could thus help to inform on RNA-based molecular solutions to help plants to adjust to a changing climate.
Job description
The position is available for a 3-year period and your key tasks as a PhD student at SCIENCE are:

• To manage and carry through your research project 
• Attend PhD courses
• Write scientific articles and your PhD thesis
• Teach and disseminate your research
• To stay at an external research institution (Cold Spring Harbor Laboratory, USA) for a few months
• Work for the department

Applicants should hold an MSc degree in Biology/Biochemistry/Molecular Biology/Bioinformatics or related fields with very good results and good English skills. As criteria for the assessment of your qualifications emphasis will also be laid on previous publications (if any) and relevant work experience, particular in the area of NGS data analysis.

The starting salary is currently at a minimum DKK 333,464 (approx. €44,461) including annual supplement (+ pension at a minimum DKK 54,191). Negotiation for salary supplement is possible.