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Dissecting the role of DNA methylation in spiral cleavage


Project Description

Nearly all animals originate during a process called embryogenesis, in which a single cell – the zygote – develops into a multicellular complex organism. This is a stepwise process, where the zygote first divides and defines a primary set of progenitor cells, which later on differentiate into the wealth of cell types, tissues, and organs of adult animals. Which cellular and genetic mechanisms control animal embryogenesis? How do these mechanisms evolve over time? How does its change contribute to animal evolution? Dr Martin’s lab investigates how the diversity of early embryonic strategies found in Spiralia – one of the largest groups in animal phylogeny, including clades such as molluscs and annelids – informs these questions.

DNA methylation is the addition of methyl groups to cytosines (4mC, 5mC) and adenosines (6mA), and it is a major mechanism for regulating gene expression in mammals. Altered in prevalent human diseases like cancers, DNA methylation (5mC) is critical during early mammalian embryogenesis, in particular during cell fate differentiation. While common invertebrate biomedical systems, such as Drosophila and C. elegans, lack this epigenetic mark, spiralians exhibit significant levels of DNA methylation (5–20%). Dr Martin’s lab uses annelid worms as model species to study early spiral cleavage, combining genomics, epigenomics, and classic embryological approaches. In collaboration with Dr Robert Lowe, an Alan Turing Institute Fellow, whose group is developing machine-learning-based computational tools to profile and investigate the role of DNA methylation in animal genomes, we want to pioneer the study of DNA methylation in spiralians. Not only will this dissect the role of a key epigenetic mark in a major branch of the animal tree of life, but also provide a fundamental understanding of the role of an epigenetic mechanism prevalent in many human disorders.

A PhD studentship is available for a collaborative project between Dr Martin’s and Dr Lowe’s labs that studies the role of DNA methylation in the epigenetic control of gene expression during early embryonic spiral cleavage. The project will generate genome wide DNA methylomes and investigate the role of the DNA methylation machinery during annelid spiral cleavage. Dr Martin’s and Dr Lowe’s labs work with a variety of animal and protist systems, and thus the successful applicant will also have some opportunity to develop his/her own research directions based on interests and skills, given that these fall within the expertise of the supervisors and align with on-going research projects.

We are looking for a highly self-motivated and enthusiastic candidate with a strong interest in epigenomics and evolutionary developmental biology, some research experience in molecular biology, and some previous computational experience (literacy in Unix environments and programming languages such as R, python or C/C++). The project will involve both experimental and computational approaches, as well as molecular biology and embryological techniques. The successful applicant will also have the opportunity to present their work at national and international conferences, and to collaborate with other research groups at an international and interdisciplinary level. The successful candidate will need to be able to work independently, as well as part of a team. While training will be available, the student will also be expected to develop proficiency in molecular techniques (e.g. nucleic acid extraction, gene cloning, in situ hybridization, immunohistochemistry, epigenomic approaches), and computational analyses of next-generation sequencing datasets.

Location: Dr Martin’s group is based at Queen Mary’s School of Biological and Chemical Sciences (Mile End campus), and Dr Lowe’s group is based at Queen Mary’s Blizard Institute (Whitechapel campus). Queen Mary is a Russell Group University, a college of the University of London and located in London’s vibrant East End (10 min bicycle ride to Tower Bridge; 10 min walking to Victoria Park; 30 min walking to Shoreditch nightlife). It benefits from state-of-the-art equipment and expertise in molecular biology, next-generation sequencing technologies, genomics, and bioinformatics.

Applications should include a statement of purpose (motivation letter), a CV, transcripts, and two referee details.

Informal enquiries are encouraged and can be made by email to Dr Chema Martin () and Dr Robert Lowe (). For more information about Dr Martin’s research profile, please see https://www.martinduranlab.com . For more information on Dr Lowe’s research profile, please see https://www.qmul.ac.uk/blizard/staff/centre-for-genomics-and-child-health/staff/robert-lowe.html.

Funding Notes

Applications are invited from candidates with, or expecting to be awarded, a degree (UK 1st or 2:1 or equivalent qualification) in a relevant area (e.g. biology, biochemistry, biomedicine). Although not essential, ideally applicants will have a Master’s degree, or appropriate relevant work experience. Experience in molecular biology, microscopy, and/or bioinformatics are desirable. Students outside the UK are required to provide evidence of their proficiency in English language skills.

The studentship will cover tuition fees and provide an annual tax-free maintenance allowance for 3 years at the Research Council rate (£16,777 in 2018/19).

How good is research at Queen Mary University of London in Biological Sciences?

FTE Category A staff submitted: 23.39

Research output data provided by the Research Excellence Framework (REF)

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