PhD position (Epigenetics & Nuclear Dynamics, RNA Biology): Mass Spectrometry of Epigenetic DNA Modifications

    International PhD Programme “Gene Regulation, Epigenetics and Genome Stability”
    Biological sciencesBiology
    First Stage Researcher (R1)
    27/11/2020 23:00 - Europe/Brussels
    Germany › Mainz


Thinking of doing your PhD in Molecular Biology? The International PhD Programme (IPP) on Gene Regulation, Epigenetics & Genome Stability is offering talented, young scientists the chance to work at the cutting edge of research. The IPP is a community of exceptional scientists working on diverse topics ranging from how organisms age or how our DNA is repaired, to how epigenetics regulates cellular identity or neural memory.

The programme is coordinated by the Institute of Molecular Biology (IMB) — a modern research centre located on the bustling campus of Mainz University in Germany. With a population of 200,000, of which about 40,000 are students, the city of Mainz is charming and open-minded and is within easy reach of cosmopolitan Frankfurt, the Rhine valley region with its castles, vineyards, and nature reserves, and the equally picturesque cities of Wiesbaden and Heidelberg. With Frankfurt airport – the largest airport in mainland Europe – only 20 minutes away, countless European and overseas destinations are within easy reach.

Activities and responsibilities:

In the field of “Epigenetics & Nuclear Dynamics” and “RNA Biology”, the IPP research group of Prof Dr Christof Niehrs offers the following PhD project:

Mass Spectrometry of Epigenetic DNA Modifications

Not only RNA but also DNA is modified in cells to regulate gene activity epigenetically. For example 5’-methylcytosine (5mC) serves as an epigenetic modification, which provides a memory state for silencing gene expression. We utilize highly sensitive mass spectrometry (Triple Quadrupole Mass Spec) and non-radioactive stable isotope metabolic labelling to profile DNA modifications, including 5mC, 5hmC, 5fC, 5caC, m6A, and others.

Figure 3: Principle of analysis of RNA modifications by LC-MS/MS

PhD project

The successful candidate will have a strong background in Organic Chemistry or Biochemistry to study nucleic acid modifying enzymes to unravel how chemical modifications in genomic DNA and DNA:RNA hybrids (“R-loops”) regulate pluripotency and differentiation of mammalian embryonic stem cells and embryos. You will use LC-MS/MS, genome-edited CRISPR/Cas9 stem cell mutants, as well as various NGS protocols to carry out a multi-dimensional analysis to address: Which modifications can be identified and how do they change with different cellular states? What enzymes mediate them? Where in the genome do the modifications occur? What are molecular determinants involved in targeting of modifications to specific sites? Critical methods you will use are LC-MS/MS, embryonic stem cell self-renewal and pluripotency, CRISPR/Cas9 mediated genome editing, as well as Next generation sequencing (NGS) methods. The project will involve strong interaction with computational biologists.

What we offer:

  • Exciting, interdisciplinary projects in a fully international environment, with English as our working language
  • Advanced training in scientific techniques and professional skills
  • Access to our state-of-the-art Core Facilities and their technical expertise
  • Fully funded positions with financing until the completion of your thesis.
  • A lively community of more than 140 PhD students from 40 different countries


Are you an ambitious, young scientist looking to push the boundaries of science while interacting with colleagues from multiple disciplines and cultures? Then the IPP is your opportunity to give your scientific career a flying start!

We seek enthusiastic candidates with a special interest in the following topics:

  • Ageing & Disease
  • Bioinformatics & Computational Biology
  • DNA Repair & Genome Stability
  • Epigenetics & Nuclear Dynamics
  • Gene Regulation & Evolution
  • RNA Biology

Further requirements:

  • Master or equivalent
  • Interactive personality & good command of English
  • 2 letters of reference

For more details on the projects offered and how to apply via our online form, please visit


The deadline for applications is 27 November 2020. Interviews will take place in Mainz on 25-27 January 2021 if the pandemic situation allows. Otherwise we will inform selected candidates in due time about an alternative online programme.

Starting date: 1 March 2021 – 1 September 2021

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1 position(s) available at
International PhD Programme “Gene Regulation, Epigenetics and Genome Stability”
Ackermannweg 4

EURAXESS offer ID: 559010


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