PhD Scholarship in CRISPR-mediated Gene Editing Combined with Proteomics to Study the Function, Structure, Regulation and Targeting of Nuclear Exosome Adaptor Complexes in RNA Decay

University of Southern Denmark
April 01, 2023
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PhD Scholarship in CRISPR-mediated Gene Editing Combined with Proteomics to

Study the Function, Structure, Regulation and Targeting of Nuclear Exosome Adaptor Complexes in RNA Decay

PhD Scholarship in CRISPR-mediated Gene Editing Combined with Proteomics to

Study the Function, Structure, Regulation and Targeting of Nuclear Exosome Adaptor Complexes in RNA Decay

The Centre for Exo-Adapt invites applications from outstanding candidates who are interested in joining our team as a PhD fellow. The PhD fellow will be affiliated with the Jens S. Andersen group at the Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense. The position is available for three years from May 2023 or as soon as possible thereafter. Application deadline: 1 April 2023.

The RNA Exosome Our genome produces RNA that either gives rise to protein or to independent RNA molecules. However, genomic DNA is hyperactive, and only a fraction of the RNA produced ends up as functional molecules - the rest is degraded. The exosome complexes are the molecular machines that detect and remove undesirable RNA so that cells do not drown in their own molecular waste? The core complex of the exosome has been comprehensively studied, revealing that it is merely a general RNA degradation machine. Instead, specific recognition of its multitude of substrates is achieved by the association of the exosome with so-called protein adaptor complexes. Although some of these have been identified, we do not understand how they recognize and discriminate their substrates, how they interact with the exosome and how these interactions are regulated to achieve adequate RNA turnover at steady state or in dynamic cellular settings.

Exo-Adapt The Centre for Exo-Adapt is a collaborative project supported by a grant from the Novo Nordisk Foundation Challenge Programme. The Exo-Adapt initiative aims to study the function, structure, regulation, and targeting of nuclear exosome adaptor complexes with a role in RNA degradation using a combination of genomics, proteomics, and cryo-electron microscopy approaches.

The project involves the following PIs:

  • Torben Heick Jensen (coordinator), Department of Molecular Biology and Genetics, University of Aarhus, Denmark
  • Elena Conti, Max Planck Institute of Biochemistry, Munich, Germany
  • Jens S. Andersen, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
  • Research Project and Role As a PhD fellow in Exo-Adapt you will be involved in highly ambitious and interdisciplinary projects covering functional and structural studies of protein-RNA complexes using for example CRISPR-mediated gene editing for tagging op proteins for protein-protein interaction and protein proximity labelling analysis, fluorescence microscopy, and PTM analysis by mass spectrometry-based proteomics, and characterization of RNA substrates by RNA sequencing and bioinformatic approaches.

    You will interact and collaborate closely with other researchers in the Jens S. Andersen, Torben Heick Jensen, and Elena Conti groups as well as with members of the other research groups at the Biomedical Mass Spectrometry and Systems Biology Section at the Department of Biochemistry and Molecular Biology.

    We offer:

  • A research position available for three years in a stimulating and supportive, international research environment.
  • Access to state-of-the-art equipment, facilities, and infrastructure within proteomics, including a unique collection of advanced instrumentation for mass spectrometry (Orbitrap Exploris 480 and Orbitrap Eclipse from Thermo Fisher Scientific, and timsTOF Pro and flex from Bruker) and for bioimaging (Abberior facility line STED, MINFLUX, Nikon 3D STORM and Nikon dual cam SIM).
  • Opportunity to exchange knowledge, discuss project progress, and visit Exo-Adapt partners for cross-laboratory research projects and environmental exchange as part of the PhD education.
  • Opportunity to interact with a wider network of national and international collaborators.
  • Opportunity to develop your own ideas within our research frame.
  • A competitive salary and social benefits (e.g. health coverage, parental leave, social security etc.).
  • Dedicated assistance and support with various practical, social, and legal aspects (housing, visa, administration, tax etc.), especially for international candidates through our international staff office (ISO) and department.
  • For further information please contact Professor Jens S. Andersen, e-mail: [email protected]

    Application, salary etc. Appointment as a PhD Research Fellow is for three years. Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period.

    The successful applicant will be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations). Please check links for more information on salary and taxation.

    The successful candidate will be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).

    The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

    Application must be in English and made in the form of a Declaration of Interest including the following: • A research proposal/description of your approach to the above project (max one page excluding references) • A letter stating your specific interest, motivation and qualifications for the project in question (max. two pages) (please attach this under box "Application form") • Detailed CV, including personal contact information • Copies of diplomas, Bachelor as well as Master's degree, including transcript of notes/grades • At least two signed reference letters. Should your referees wish to send their letters directly to us, please have them use e-mail: [email protected] mentioning your name and the title of the position in the subject line. And please note that these also need to reach us before deadline.

    Shortlisting may be used in the assessment process.

    Further information about the PhD-study can be found at the homepage of the University.

    Applications must be submitted electronically using the link "Apply online". Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read How to apply before you apply.

    Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.

    Further information for international applicants about entering and working in Denmark.

    Campus: Odense

    Application deadline: 01/04/2023

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