PhD Student in Epigenetics and Chromatin Dynamics – Lund University

Job Description

The Laboratory of Epigenetics and Chromatin Dynamics at the Department of Experimental Medical Science (Faculty of Medicine), is currently conducting research investigating the epigenetic regulation of repetitive and transposable genetic elements – so-called 'genomic dark matter' – in human brain development and disease. The group consists of 8 research-active members and is led by Dr Christopher Douse. We are fascinated by how these underexplored regions of the human genome contribute functionally to human neurobiology and neurological disease. Our work integrates state-of-the-art wet and dry lab methods. More information can be found here . As a workplace, we safeguard a good work environment with respect and consideration in our relationships with each other. We commit to the following core lab values: Equity – all lab members have value and contribute, there are no stupid questions; People-centric - our work is collaborative and we communicate openly with eachother, the community and the outside world; Integrity – we do not take shortcuts and emphasize reproducibilty and rigor in our data. Curiosity - we are humble about what we don't know, actively seek feedback and are open to ideas; Diversity – we will do better research if we have diversity of background and scientific expertise.

Project description
We are particularly focused currently on three types of element that are repetitive in different ways, but unified by an importance to human brain function and disease: clustered protocadherin repeat genes, viral-like sequences called retrotransposons, and CGG microsatellite tandem repeats. In all cases there are significant knowledge gaps surrounding the epigenetic control and influence of the elements. What are the factors that bind and regulate these REs in neural lineages? How do they functionally impact the epigenome and local transcriptional dynamics, and disease traits? To answer these questions we will combine chromatin biochemistry and cutting-edge functional epigenomics with advanced neural cellular models and tailored bioinformatic analyses. In doing so we will discover new, basic human neurobiology and much-needed insights on the mechanisms underpinning RE-associated neurological disorders.
This PhD project will combine chromatin biochemistry with functional (epi)genomics in stem cell models of the human brain. Importantly, this PhD project will require a balance of wet and dry-lab approaches.
In particular the doctoral student will use the following methods:
• Stem cell culture (iPSCs, 2- and 3D neural progenitors)
• RNA-seq, CUT&RUN/Tag, Oxford Nanopore sequencing (cDNA, DiMeLo-seq) and associated bioinformatic analyses
• Co-immunoprecipitation and/or proximity labelling proteomics

Tasks and responsibilities
The main task for a doctoral student is to devote yourself to your doctoral studies, therefore you will be both admitted as a student and employed at Lund University. In addition to your full-time research studies, you may be involved in the supervision of bachelor or master students.

Qualifications

• Requirements for admission:
• a second-cycle degree, completed course requirements of at least 240 higher education credits, of which at least 60 higher education credits are at second-cycle level, or substantially equivalent knowledge acquired in Sweden or abroad
• the ability to benefit from doctoral studies
• Requirements for the position:
• experience in functional (epi)genomics and/or chromatin biochemistry
• experience with stem cell culture and differentiation models
• a demonstrable interest in the repetitive genome, either in humans or model organisms, through previous experience or as described in your cover letter or during an interview
• excellent knowledge of molecular biology and molecular genetics
• excellent spoken and written English
• good analytical skills and an independent, problem-solving approach
• an open and collaborative approach to research, in line with the lab values described above

Skills Required

• being highly organised and self-motivated
• experience with long-read sequencing approaches
• experience with protein biochemistry
• experience working collaboratively on ambitious research projects
• being receptive to constructive feedback and demonstrating a willingness to develop and learn throughout the doctoral studies

Additional Information

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