PhD position: CRISPR-Associated Endonucleases for Therapeutic Genome Editing (m/f/d)PhD – Individual Supervisor

  • Contract
  • Germany
  • Posted 2 months ago

Insitute of Molecular BiologyInternational PhD Programme


Thinking of doing your PhD in the Life Sciences? The International PhD Programme (IPP) Mainz is offering talented, young scientists the chance to work on cutting edge research projects. As an IPP PhD student, you will join 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.

Activities and responsibilities

In the field of “DNA Repair & Genome Stability”, the research groups of Anton Khmelinskii and Vassilis Roukos offer the following PhD project:

CRISPR has revolutionized both basic and applied biomedical research as an exceptional tool for programmable, targeted and precise genome editing. The DNA-targeting specificity of the CRISPR-associated endonuclease Cas9 has been enhanced by redesigning guide RNAs (gRNAs) and engineering variants with higher fidelity. However, control of Cas9 template-free editing in eukaryotic cells remains suboptimal for high precision therapeutic applications.
The repair outcome (the insertions and deletions, indels, associated with repair) of Cas9-induced DNA double strand breaks (DSBs) is not random but depends strongly on the sequence context of the target site, the type of DSB produced by Cas9 and can be modulated by mutations in Cas9 itself. The Roukos group recently developed novel Next-Generation Sequencing (NGS)-based methods to characterize alternative Cas9 cleavage patterns and established that certain types of Cas9 cuts are repaired by the cellular machinery to produce templated and predictable editing outcomes (Longo et al., submitted). The frequency of certain types of Cas9 induced DSBs varied greatly between target sites, and could be further modulated by mutations in Cas9 (Longo et al., submitted). These findings establish a clear mechanistic link between the type of DSB generate by Cas9 and repair outcome, and provide a unique opportunity for optimization of Cas9 towards predictable and precise gene editing, forming the basis of this PhD project.

PhD Project: “Engineering CRISPR-Associated Endonucleases for Precise and Predictable Therapeutic Genome Editing”

This project aims to engineer Cas9 variants that generate exclusively certain types of DSBs, allowing a predictable repair outcomes independently of the target sequence. For that we will establish fluorescent reporters for desirable repair outcomes in both yeast and human cells. We will use these reporters to perform targeted deep mutational scanning and random mutagenesis of Cas9 to identify Cas9 mutations with increased rates of desired outcomes and examine applications of such Cas9 variants for precise genome editing, including generation of gene knockouts and correction of disease variants in patient cells. The project combines work with both yeast and mammalian cells, and training on molecular, cellular and NGS-based methodologies. It combines the interests and expertise of the Roukos group in CRISPR biology and the development of genome-wide methods profiling Cas9 DNA incisions, the expertise of the Khmelinskii group in high-throughput screening and deep mutational scanning approaches, and the mutual interests in genome engineering.

If you are interested in this project, please select Khmelinskii/Roukos as your group preference in the IPP application platform.

Qualification profile

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

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

We offer

  • Exciting, interdisciplinary projects in a lively 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 190 PhD students from 44 different countries

For more details on the projects offered please visit  .

The deadline for applications is 8 November 2023. Interviews will take place at IMB in Mainz on 22-24 January 2024.
Starting date: 1 March 2024 – 1 August 2024

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