Project description
A closer look at cell identity in vertebrate genomes
The complexity of vertebrate genomes presents a challenge: despite having tens of thousands of genes, only a few stable cell types are produced. Understanding how these cell types are encoded remains a puzzle. Gene regulatory elements, which control gene expression, play a crucial role but are less conserved than genes and can be far from their target genes. Supported by the Marie Skłodowska-Curie Actions programme, the EvoDCode project explores how genomic sequences dictate cell identity in the pallium across vertebrates. Using cutting-edge single-cell sequencing and machine learning models, the project aims to map regulatory elements and their role in species-specific and conserved cell types, providing new insights for evolutionary biology and therapeutic applications.
Objective
Vertebrate genomes consist of tens of thousands of genes and yet they produce only a limited number of stable cell types. Our understanding of how cell types are encoded in the genome is still lacking. The expression of genes is controlled by gene regulatory elements, which are evolutionarily much less conserved than genes are and can be located far away in the genome. My main goal is to better understand how the genomic sequence underlies cell identity in the pallium across vertebrate species and I hypothesize that gene regulatory logic can be directly learned from the genomic sequence and used to predict cell types. Recent advances in the field of single cell sequencing have made the generation of large epigenomic datasets possible, while novel machine learning models like DNA language models are providing unprecedented insights into the regulatory logic of the genome. In addition, for many non-model species high quality reference genomes are becoming available as there is an increased awareness for the need to preserve biodiversity.
I will conduct single cell multiome sequencing, supplemented with low-cost single-cell ATAC-seq using the HyDrop platform - developed in the host-lab - to profile regulatory elements across cell types in the pallium from multiple species, including mammals, birds, lizards and fish. My experience in generating and annotating single cell data from the brain will aid in the analysis and alignment of the generated datasets. Next, I will use this data to study the relationships between the genome of a species and the identified cell types by training species-aware DNA language models and using these models to identify species-specific and conserved regulatory logic. These models will not only be interesting from an evolutionary perspective, but also aid in ongoing efforts to develop synthetic enhancers used to target highly specific cell types, which can be applied in many therapeutic applications.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
- natural sciences biological sciences genetics DNA
- natural sciences biological sciences ecology ecosystems
- natural sciences biological sciences zoology mammalogy
- natural sciences biological sciences genetics genomes
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Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Programme(s)
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
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HORIZON.1.2 - Marie Skłodowska-Curie Actions (MSCA)
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Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Funding Scheme
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Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
HORIZON-TMA-MSCA-PF-EF - HORIZON TMA MSCA Postdoctoral Fellowships - European Fellowships
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Call for proposal
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(opens in new window) HORIZON-MSCA-2024-PF-01
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9052 ZWIJNAARDE - GENT
Belgium
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