STUDYING ENHANCER AT ALL SCALES – Deciphering the molecular basis of human enhanceropathies
ESR 2 project : Modeling gene-environmental interactions implicated in the etiology of human neurocristopathies (WP3)
Using human neural crest cells and the TFAP2A locus as a medically relevant models, our work will evaluate whether genetic variants within enhancers might interact with teratogenic factors as part of the etiology of human congenital abnormalities. Thus, by considering enhancers as hubs of gene-environmental interactions, our results can illuminate a novel and broadly relevant etiological paradigm for human disease.
Supervisor : Alvaro Rada-Iglesia
Vice-coordinator & WP4 Leader
University of Cantabria
ESR 3 project : Genetic and epigenetic changes in hematopoietic stem cells (HSCs) during chronic inflammation (WP3)
This project will determine the molecular changes in enhancers and promoters that chronic inflammation induces in hematopoietic stem cells. Together, the results of this project will uncover the mechanisms regulating hematopoietic stem cell maintenance and fate in the context of chronic inflammation, and lay the path to identify new therapeutic strategies.
Supervisor : Meritxell Alberich-Jorda
Institute of Molecular Genetics, Prague, Czech Republic
ESR 6 project : Computational approaches to discover noncoding mutations underlying human disease (WP3)
Human genetics is rapidly moving from the analysis of protein-coding sequences to whole genome sequences. Our ability to discern non-protein coding mutations that cause disease from a vast excess of non-functional mutations is still limited. This PhD project will focus on an ERC-funded large-scale enhancer mutation screen in patients with monogenic diabetes. It will develop computational approaches to inform on the pathogenicity and function of enhancer mutations, using data from ongoing experimental and patient screens.
Applicants with diverse educational backgrounds are welcome, but a computing background is important, including basic knowledge of a programming language (e.g Python, R). Expertise in statistical analysis is also highly relevant.
Supervisor : Jorge Ferrer
ESR 11 project : Functional understanding of synergistic effects of enhancer elements at the onset of atherosclerosis (WP3)
The aim of the project is to establish a method that can resolve multiple promoter-anchored interactions at single cell resolution. The method will utilise droplet technology and chromatin immunoprecipitation to identify multiple promoters and enhancers contacts. Such data will help elucidate to which degree enhancers cooperate in regulating expression of their target genes, and contribute to our understanding of the role of enhancer redundancy in complex diseases context. We will apply the methodology to aortic endothelial and smooth muscle cells, liver cells and activated macrophages to study the extent of redundancy in regulatory networks concerning cardiovascular risk variants.
Supervisor : Pelin Sahlén
Royal Institute of Technology
ESR 15 project : Uncovering drug-adaptive epigenetic response in Acute Myeloid Leukemia (AML) (WP3)
This project will uncover drug-responsive regulatory elements and related molecular mechanisms that may have an impact on AML therapeutic outcomes and drug resistance. These results can pave the way to strategies with improved therapeutic efficacy by targeting of enhancers or their targets with inhibitors that can attenuate the adaptive transcription to genes related to drug resistance and proliferation.
Supervisor : Mileidys Perez
Legal Supervisor : SALVATORE SPICUGLIA
ESR 4 project : The impact of genetic variants on regulatory activities (WP3)
This project aims to explore the impact of regulatory genetic variation. In particular, the major aims are to establish accurate and interpretable machine learning approaches to learn how DNA sequence influences enhancer and promoter activities and to use derived models to interpret the determinants of regulatory function and the impact of regulatory genetic variation on their activities in health and disease. To this end, part of the project will focus on in vivo (CAGE, ATAC-seq, Hi-C) and in vitro (STARR-seq, SURE-seq) data generated in our lab and within the ENHPATHY network across a genotyped panel of lymphoblastoid cell lines, displaying large individual regulatory variation. Inferred models will further our understanding of the determinants of regulatory function and improve genetic variant interpretation, which will be useful for a large scientific and medical community, ultimately leading to insights into why and when regulatory genetic variation may cause phenotypical or pathological changes.
Supervisor : Robin Andersson
University of Copenhagen
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