ChromDesign is an innovative and interdisciplinary network of 10 European academic and private institutions that will characterize how 3D chromatin organization affects gene regulation during cellular differentiation and in several human disorders. We will train 13 Early Stage Researchers (ESR), equipping them with the skills, knowledge, expertise, and enthusiasm necessary to develop successful future careers in the biomedical field (in academia or the private sector). Together with European experts in chromatin biology, 3D genomics, and research design, these ESRs will work towards the goal of identifying novel alterations in chromatin topology responsible for cellular malfunctions to: i) develop new diagnostic tools, ii) effectively communicate research results through specific toolkits; and iii) identify novel therapeutic targets with the potential to be exploited as treatments. Alteration of gene regulation occurs naturally during aging and underlies several human diseases. Its better characterization requires a deeper understanding of the spatial organization of the genome. We will investigate how the genome organizes in 3D over time, and how the 3D organization is related to gene regulation in health and disease. We will use and develop technologies in imaging, cell biology, genomics, and computational modelling and will focus on translating our results into clinical applications. ESRs will thereby receive training with state-of-the-art technologies in distinct research areas and in modules with theoretical and hands-on sessions on transferable skills: entrepreneurship, management, communication, and outreach. ChromDesign comprises 6 work packages: WP1–4 address the 4 main areas of chromatin biology and 3D genomics; WP5 applies the knowledge obtained from WPs1–4 into translational research; WP6 develops (with a dedicated ESR) a set of design toolkits for communicating results to scientists, the public, and schools; and WP7 ensures quality training for ESRs.