Fig. 2

3D chromatin organisation and deregulated transcription in tumorigenesis. Schematic depiction of the different levels of chromatin organisation including chromosome territories in the nucleus, lamina-associated domains (LADs) near the nuclear envelope, A and B compartments corresponding to open and closed chromatin, and a topologically associated domain (TAD) with the 3D chromatin looping in the TADs that can be visualised as chromatin interaction maps (red triangles in TAD). Tumorigenesis involves a range of changes impacting 3D chromatin architecture such as LAD defects, TAD boundary defects, and changes in enhancer–promoter (E–P) interactions regulating gene induction or silencing, as well as lower-order chromatin changes involving transcription factor availability, histone modifications, DNA methylation/hydroxymethylation, nucleosome occupancy, and involvement of long non-coding RNAs (lncRNAs) and micro-RNAs (miRNAs)