PhD Candidate in Epigenetics & Gene Regulation

Epigenetic regulation of cell identity is essential for cell functionality and tissue homeostasis. Understanding the dynamics of epigenetic programming holds significant impact for deciphering the complexities of disease and developmental processes. If you share our fascination for this captivating process, join our team and embark on this exciting journey together!

Within this project we aim to unravel the gene regulatory mechanisms of a newly identified chromatin bound protein that acts as a dynamic switch between opposite epigenetic histone marks H3K27me3 (repressive) and H3K79me2 (activating). We will assess this both in human cancer cell lines and mouse developmental models (mouse embryonic stem cells and gastruloids). 

The project, led by Dr. Rutger Gjaltema, is embedded in the Molecular & Cellular Epigenetics (MCE) group at the Swammerdam Institute for Life Sciences (SILS) and in close collaboration with Dr. Thijs van Boxtel (Developmental, Stem Cell and Cancer Biology Group, SILS). 

The mission of the Molecular & Cellular Epigenetics group is to understand the influence of dynamics and cell-to-cell variability of epigenetic regulation particularly in the context of cell decision making and responsiveness. Regarding heterogeneity in cell responsiveness of cell populations, we are specifically interested in the role of broad epigenetic domains and transcription bursting. 

We employ state-of-the-art tools such as CRISPR/dCas9 epigenome editing, ATAC-seq, CUT&Tag, (nascent) RNA-seq, single-molecule and real-time single cell advanced microscopy, and functional genomics tools including CRISPR/Cas9 genome editing and degron systems. Wet lab tools are combined with computer simulation, machine learning and bioinformatics. 

What are you going to do? 

You will generate human and mouse cell lines with genomic integrated reporters and degron-based acute protein depletion systems. Furthermore, you will apply state-of-the-art NGS-tools on these cell lines to quantify chromatin accessibility, epigenetic marks and nascent transcription to distill the epignetic mechanism of the novel chromatin regulator. Also, its binding partners will be validated by co-immunoprecipitations. Finally, you will address the resulting mechanism in developmental model systems (mESCs and gastruloids) to unravel its spatiotemporal epigenetic patterns in relation to epigenetic memory formation and dissolution during early development.

Tasks and responsibilities: 
•    complete a PhD thesis within 4 years;
•    be an active member of our research group and take responsibility for shared tasks;
•    maintain an open and organized work environment;
•    keep accurate records of experiments and data by thorough documentation;
•    stay up to date with latest literature and technological developments;
•    present your results at (inter)national scientific meetings;
•    assist in teaching and supervising Bachelor and Master students;
•    take a leading role in writing and publishing manuscripts.

In addition to these responsibilities, you will have the opportunity to join an Amsterdam-based graduate school that supports you with a variety of courses for professional development. Within our group and SILS we value a positive and stimulating work environment and support crossover knowledge fertilization through various thematic meetings and social activities.

What do you offer? 

You are a person that has:
•    a MSc degree in Molecular biology or Biomedical Sciences;
•    drive and passion for epigenetic/chromatin research
•    preferential experience with molecular cloning, CRISPR/Cas9 genome editing,

     ChIP-seq/CUT&Tag/ATAC-seq, qRT-PCR, NGS library preparation, and (mESC) cell culture;
•    interest to perform bioinformatic analyses in R and bash;
•    talent for setting up and developing new molecular tools and techniques;
•    intrinsic motivation to keep learning and improving;
•    fluent capabilities in English, both written and spoken.

If you have (documented) experience with mammalian epigenetics and gene regulation but are not sure if you fit our preferred profile, don’t hesitate, and apply!

Our offer 

A temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.

Your salary will range between €2,770 in the first year to €3,539 gross per month in the last year of employment, on the basis of a full working week of 38 hours. This sum does not include the 8% holiday allowance and the 8.3% year-end allowance. A favorable tax agreement, the 30% ruling, may apply to non-Dutch applicants. The Collective Labour Agreement for Dutch Universities (CAO NU) is applicable.

Besides the salary and a vibrant and challenging environment at Amsterdam Science Park, we offer you multiple fringe benefits:
•    232 holiday hours per year (based on fulltime);
•    multiple courses to follow from our Teaching and Learning Centre;
•    a complete educational program for PhD students;
•    a pension at ABP for which UvA pays two third part of the contribution;
•    the possibility to follow courses to learn Dutch;
•    help with housing for a studio or small apartment when you’re moving from abroad. 

Are you curious about our extensive package of secondary employment benefits like our excellent opportunities for study and development? Take a look here .

Questions?

Do you have questions about this vacancy? Or do you want to know more about our organisation?

Please contact: Dr. Rutger Gjaltema, email [email protected]

About us 

The Faculty of Science has a student body of around 7,000, as well as 1,600 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain. 

The Swammerdam Institute for Life Sciences (SILS) is located at the vibrant Amsterdam Science Park. SILS is one of eight institutes of the University of Amsterdam's Faculty of Science (FNWI). With around 240 employees, SILS carries out internationally high-quality life science research and provides education within various university programs. Research is also carried out in close cooperation with the medical, biotech, chemical, flavor, food & agricultural, and high-tech industries, and revolves around 4 main themes, Cell & Systems biology, Neurosciences, Microbiology and Green Life Sciences.

Application

Do you recognize yourself in the job profile? Then we look forward to receiving your application by 21 March 2024. You can apply online by using the link below.  

Applications should include the following information (all files should be submitted in one single pdf file):
•    a letter of motivation;
•    a detailed CV including the months (not just years) when referring to your education and work experience;
•    the names and contact information of two references (no letters of recommendation are required at this stage)

We will invite potential candidates for interviews in April 2024.

A knowledge security check can be part of the selection procedure.
(for details: National knowledge security guidelines )

The UvA is an equal-opportunity employer. We prioritize diversity and are committed to creating an inclusive environment for everyone. We value a spirit of enquiry and perseverance, provide the space to keep asking questions, and promote a culture of curiosity and creativity.