Project 9: Single-cell translation dynamics following targeted smORF base editing (Alexander van Oudenaarden)

ORFeus doctoral network; Utrecht; On-site; EUR 36,000 - 45,000; Full time

Benefits offered by this job

Pension

Paid leave

Relocation support

Secondment

Job summary

The Hubrecht Institute in Utrecht invites applications for a PhD position within the ORFeus network to study translation regulation at single-cell resolution using CRISPR-based smORF editing and single-cell ribosome profiling in organoid models.

You will join a world-class supervisory team, participate in secondments, and enroll in Utrecht University’s doctoral program; the role includes 36 months full-time funded employment under MSCA with mobility and family allowances.

Qualifications

• Master's degree (or equivalent) in life sciences or related field.
• Hands-on experience with molecular biology techniques (CRISPR editing, sequencing).
• Desirable: single-cell methods, ribosome profiling, organoid culture, data analysis (R/Python).
• Good written and spoken English.
• Willingness to travel for secondment and network events.

Responsibilities

• Adapt Perturb-seq vector designs to detect guide RNAs and translation profiles in single cells.
• Validate ribo-perturb-seq using smORF variants across cell lines.
• Apply technology to organoid models and coordinate designs with other DCs.
• Collaborate across the ORFeus network and contribute data to the ORFeome platform.

Job description

The position

Small open reading frames (smORFs) scattered across the genome are translated into microproteins that standard reference catalogs miss, and these and other elements of the dark proteome can help regulate translation differently from one cell to the next. Most methods read out translation in bulk, averaging over many cells and hiding the cell-to-cell differences that matter during processes such as neural differentiation. Measuring how a targeted change to a smORF alters translation in individual cells, and doing so at scale, is an open experimental problem at the heart of dark proteome research.

This project will establish an integrated framework that studies translation regulation at single-cell resolution by combining CRISPR-based smORF editing with single-cell ribosome profiling. The novel 'ribo-perturb-seq' approach detects guide RNAs and translation profiles simultaneously in single cells and will be applied to organoid models to investigate translation regulation during neural differentiation. It is a key enabling technology of ORFeus Work Package 2, which moves from the discovery of the dark proteome to understanding its function: the platform provides single-cell functional validation for partner projects on translational control and computational microprotein design, and it connects to partner projects on single-molecule translation mapping and AI-driven translation prediction.

Main tasks

• Adapt Perturb-seq vector designs so that guide RNAs and translation profiles can be detected simultaneously in single cells, establishing the ribo-perturb-seq platform.
• Validate the ribo-perturb-seq approach using smORF variants in various cell lines, generating a quantitative dataset that characterizes how smORF variants affect translation.
• Apply the technology to organoid models to investigate translation regulation during neural differentiation, coordinating experimental designs with the projects of other doctoral candidates (DCs) in the network, here DC7 on lncRNA translation regulation, and drawing on isoform-level translation data from DC2 to inform the single-cell analysis framework.
• Collaborate across the ORFeus network, contribute the ribo-perturb-seq framework and single-cell translation datasets to the shared ORFeome platform, and produce the project's scientific report.

Methods and platforms: CRISPR-based genome and base editing, Perturb-seq guide RNA libraries, single-cell ribosome profiling (single-cell Ribo-seq) and single-cell RNA sequencing, cell-line and organoid culture including neural differentiation models, and single-cell data analysis, contributing methods and datasets to the ORFeome platform.

Secondment: you will spend around three months at an ORFeus industry partner, applying cutting-edge single-cell proteomics to investigate translation dynamics. You will also be guided by an independent academic advisor, with the possibility of a short, primarily virtual research exchange to strengthen the project.

Your profile

MSCA eligibility

You must meet all of the following on your recruitment date:

• You do not already hold a doctoral degree. If you have defended a doctoral thesis but the degree has not yet been formally awarded, you are not eligible.
• Mobility rule: you must not have lived or carried out your main activity (work, studies, and so on) in the Netherlands for more than 12 months in the 36 months immediately before your recruitment date. Compulsory national service, short stays such as holidays, and time spent in a procedure to obtain refugee status under the Geneva Convention do not count toward the 12 months.
• You hold, or will hold before the start date, a degree that formally entitles you to enroll in a doctorate, and you can enroll in the doctoral program at the Hubrecht Institute / Utrecht University.
• Candidates of any nationality may apply. There is no limit on prior research experience, as long as you do not already hold a doctorate.

Project-specific profile

• A master's degree (or equivalent) in molecular biology, cell biology, biotechnology, genetics, biomedical sciences, or a related life-science field.
• Hands-on experimental experience in molecular biology, for example CRISPR-based editing, single-cell techniques, or next-generation sequencing library preparation.
• Desirable: experience with single-cell methods, ribosome profiling, CRISPR screening or base editing, organoid or stem-cell culture, and basic data analysis (for example R or Python), and an interest in microproteins and the dark proteome.
• Good written and spoken English.
• Motivation for interdisciplinary, collaborative research, and willingness to travel for the secondment and network events.

What we offer

A full-time employment contract for 36 months as a salaried researcher, with full social security coverage, under the rules of the Marie Skłodowska-Curie Actions. This is a paid employment contract, not a stipend or scholarship.

The salary has a living allowance and a mobility allowance, plus a family allowance if you have family obligations when you are recruited. The indicative gross salary for this position is 3.204 - 4.051 euros per month. This is what you are paid before income tax and your own social-security contributions are deducted.

Beyond salary, you will receive:

• Supervision by a world-leading, interdisciplinary supervisory team.
• A secondment of around three months with an ORFeus industry partner.
• A structured training program: network-wide schools, transferable-skills training, workshops, and international conferences.
• Enrollment in a doctoral program leading to a PhD.
• Host benefits, e.g. pension, paid leave and relocation support. For all questions related to pension benefits, please refer to the Hubrecht Institute intranet page or contact the HR department for further information

The MSCA employment contract covers 36 months of full-time, fully funded employment. In line with the host institution's doctoral policy, the host funds completion of the doctorate beyond the 36-month MSCA contract as continued employment at the standard national doctoral salary scale; terms confirmed at offer stage.

Working at the Hubrecht Institute

The Hubrecht Institute is a research institute of the Royal Netherlands Academy of Arts and Sciences (KNAW) in Utrecht, the Netherlands, focused on developmental biology, stem cell research, and single-cell approaches to gene regulation within a collaborative, international environment on the Utrecht Science Park.

You will join the group of Prof. Alexander van Oudenaarden, which develops single-cell genomics and single-cell ribosome profiling methods and has established a single-cell Ribo-seq platform for measuring translation in individual cells. You will work closely with the group of Prof. Julie Aspden at the University of Leeds, who brings complementary expertise in lncRNA translation and neuronal differentiation. You will enroll as a PhD candidate at Graduate School of Life Sciences at Utrecht University, the degree-awarding partner of the Hubrecht Institute.