Project description
Designing new bacterial targets to combat global antibiotic resistance
Studies on DNA higher-order regulatory features revealed at least two types of enhancers: lead enhancers, in which the presence of genetic variants modulates the activity of entire chromatin domains, and dependent enhancers, in which variants induce minor changes, affecting DNA accessibility but not transcription. Currently, it remains unclear which sequence features are required to establish enhancer hierarchies, and under which circumstances genetic variations result in altered enhancer–promoter interactions and differential gene expression. The EU-funded DisMoBoH project proposes to investigate the molecular mechanisms that link DNA variations to transcription factor binding, chromatin topology and gene expression response, providing data on enhancer hierarchy and sequence-specific transcription factor binding.
Objective
Numerous DNA variants have already been identified that modulate inter-individual molecular traits – most prominently gene expression. However, since finding mechanistic interpretations relating genotype to phenotype has proven challenging, the focus has shifted to higher-order regulatory features, i.e. chromatin accessibility, transcription factor (TF) binding and 3D chromatin interactions. This revealed at least two enhancer types: “lead” enhancers in which the presence of genetic variants modulates the activity of entire chromatin domains, and “dependent” ones in which variants induce subtle changes, affecting DNA accessibility, but not transcription. Although cell type-specific TFs are likely important, it remains unclear which sequence features are required to establish such enhancer hierarchies, and under which circumstances genetic variation results in altered enhancer-promoter contacts and differential gene expression. Here, we propose to investigate the molecular mechanisms that link DNA variation to TF binding, chromatin topology, and gene expression response. We will leverage data on enhancer hierarchy and sequence-specific TF binding to identify the sequence signatures that define “lead” enhancers. The results will guide the design of a synthetic locus that serves as an in vivo platform to systematically vary the building blocks of local transcriptional units: i) DNA sequence – including variations in TF binding site affinity and syntax, ii) molecular interactions between TFs, and iii) chromatin conformation. To validate our findings, we will perform optical reconstruction of chromatin architecture for a select number of DNA variants. By simultaneously perturbing co-dependent features, this proposal will provide novel mechanistic insights into the formation of local transcriptional hubs.
Fields of science (EuroSciVoc)
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CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques.
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Programme(s)
Funding Scheme
MSCA-IF - Marie Skłodowska-Curie Individual Fellowships (IF)Coordinator
1015 Lausanne
Switzerland