Researcher in Plant RNA Biology

Subject description

Plants have an amazing ability to respond to environmental challenges through intracellular regulation of their functions. While much focus had been on the roles of genes coding for proteins, plant genomes are vast, containing largely non-coding DNA with unclear functional roles for cells. Our past research revealed how the non-coding genome of plants contributes to cellular resilience mechanisms through the production of non-coding RNA molecules, or through chromatin signatures that correlate with ncRNA production.

We are looking for a researcher enthusiastic about mechanistic Plant Molecular Biology in this area. Specifically, to address the question of how chromatin signatures linked to ncRNA production can inhibit gene induction (DOI: 10.1016/j.tplants.2020.03.005 , DOI: 10.1371/journal.pgen.1007969). As starting point, we isolated mutants in chromatin modifying pathways disrupting this mechanism.

The researcher in RNA Biology will work on a project where we identified the 5´-end positions of RNA Polymerase II initiation, Transcription Start Sites (TSSs) genome-wide (i.e. using STRIPE-seq). We focused our analyses on chromatin mutants resulting in the induction of TSSs in positions where they are usually repressed, most importantly in regions where RNA polymerase II elongates, such as in gene bodies. In combination with direct RNA sequencing using Oxford nanopores, we identified fascinating examples for gene regulation, whereby TSSs induced in chromatin mutants avoid negative effects of alternative poly-adenylation (APA) in introns that prevents full-length mRNA formation.

Your role in the initial phase of this project will be to start from these existing data, and finish remaining analyses, generate and analyze CRISPR/Cas9-mediated deletions at target loci and pursue publication of this project.

Work duties

Detailed description of the work duties, such as:

• Research within Plant RNA Biology
• Teaching in the first, second and third cycles of studies
• Supervision of degree projects and doctoral students
• Actively seeking external research funding
• Collaboration with industry and wider society
• Administration related to the work duties listed above

Qualification requirements

Applicants must have:

• A PhD or equivalent research qualification within the subject of the position.
• Strong background in Molecular Plant Biology, especially RNA Biology, for example custom next-generation library protocols.
• Very good oral and written proficiency in English.
• Excellent ability to develop and conduct high-quality curiosity-driven research independently.

Assessment criteria and other qualifications

• Proficiency in Next-Generation sequencing analyses, for example, using high-performance computing, R and python.
• Interest and Passion for the outlined research project in Plant RNA Biology
• Self-motivation
• Perseverance
• Results-oriented with aim to finish projects for publication

Consideration will also be given to good collaborative skills, drive and independence, and how the applicant’s experience and skills complement and strengthen ongoing research within the department, and how they stand to contribute to its future development.

Terms of employment

This is a full-time, fixed-term employment for 1 year. Starting as soon as possible.

Contact person: Sebastian Marquardt (andreas_sebastian.marquardt@biol.lu.se).

Instructions on how to apply

Applications shall be written in English and be compiled into a PDF-file containing:

• résumé/CV, including a list of publications,
• a general description of past research and future research interests (no more than three pages),
• contact information of at least two references,
• copy of the doctoral degree certificate, and other certificates/grades that you wish to be considered.