A scaffolding element rewires local 3D chromatin architecture during differentiation

During differentiation chromatin and transcription are rewired to reflect the new cellular identity. However, what drives these changes and their mutual relationship remains unclear. Here, we use mouse ESC-to-NPC differentiation to study rewiring at a 3 Mb large Zfp608 locus. This large chromatin domain splits in half at the Zfp608 promoter, local chromatin gets littered with activating marks, compacts in 3D space and Zfp608 transcription is induced. We combine capture Hi-C (cHi-C), biophysical modelling, and 3-color 3D-FISH to investigate cis and trans elements driving this process. We find that transcription modulates both, local chromatin contacts and insulation at the domain split and we identify a genetic element with dual enhancer/architectural function essential for chromatin rewiring and loop formation, a scaffolding element. Together, these results demonstrate that a hierarchy of genetic elements in cis allows successful rewiring during differentiation and that multiple trans acting elements contribute to making this rewiring efficient. Cell differentiation induces a 3D chromatin rewiring at the Zfp608 locus, driven by active transcription and a dual-function enhancer-scaffolding element that fosters key long-range interactions using both CTCF-dependent and independent mechanisms.