Beyond TADs and Compartments: Mesoscale Chromatin Folding and Its Dynamics in Transcriptional Regulation

Below the scale of long-range compartments and topologically associating domains (TADs) lie a diverse set of local chromatin organization features. Recent maps and single-molecule assays reveal modular sub-TAD units, nucleosome clutches, micro- and nanodomains, packing domains, microcompartments, and stripes arising from an interplay of loop extrusion, epigenetic affinity and condensates, and polymerase motion. We highlight how cohesin regulation and its crosstalk with transcription shape local topology, how microcompartments and affinity-driven hubs guide enhancer–promoter communication, and how nucleosome positioning and spacing set the energetic landscape on which these forces act. We also outline how sub-TAD architecture is related to dynamics and single-molecule heterogeneity, describe additional looping mechanisms and several case studies of mesoscale structure regulation, and discuss perspectives on how technological advances can build a more mechanistic understanding of mesoscale chromatin organization. Overall, we argue that the submegabase structure of chromatin, though complex, is an essential length scale for understanding transcriptional regulation.