Decoding how the “non-coding” genome controls gene expression is one of the grand challenges of modern biomedicine. Most disease-associated variants fall in regulatory DNA, yet their effects on gene regulation remain largely unpredictable, limiting diagnosis, risk stratification and the design of safe gene and cell therapies. cisCODE is an MSCA Doctoral Network that will train 15 Doctoral Candidates to crack the cis-regulatory code by combining cutting-edge genomics with artificial intelligence and synthetic biology.
The network gathers 13 academic partners, completed with 9 non-academic partners across experimental and computational disciplines. Together, they will (i) decode the sequence “grammar” and modular function of cis-regulatory elements, (ii) map the rules of communication and compatibility between distal enhancers and promoters in three-dimensional chromatin, and (iii) build causal, predictive enhancer-based gene regulatory networks in health, stress, inflammation and cancer. Doctoral projects will leverage single-cell multi-omics, high-throughput functional assays, advanced 3D genome profiling and next-generation AI models to move from descriptive catalogues to mechanistic and predictive understanding.
cisCODE is also a training engine for Europe. A structured, international and intersectoral programme will provide Doctoral Candidates with personalised research and career development plans, network-wide schools, secondments in industry and clinics, and dedicated training in open science, data stewardship, ethics and innovation.
By delivering new models, datasets and synthetic regulatory tools openly to the community, cisCODE will accelerate interpretation of regulatory variants, support the rational design of precision therapies, and consolidate Europe’s leadership at the interface of regulatory genomics, artificial intelligence and personalised medicine.
