Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system

In single cells, variably sized nanoscale chromatin structures are observed but it is unknown if these form a cohesive framework that regulates RNA transcription. Herein we demonstrate that the human genome is an emergent, self-assembling system. Conformationally-defined heterogenous, nanoscopic packing domains form by the interplay of transcription, nucleosome remodeling, and loop extrusion. We show that packing domains are not topologically associated domains. Instead, packing domains exist across a structure-function life-cycle that couples heterochromatin and transcription in situ, explaining how heterochromatin enzyme inhibition can produce a paradoxical decrease in transcription by destabilizing domain cores. Applied to development and aging, we show the pairing of heterochromatin and transcription at myogenic genes that could be disrupted by nuclear swelling. In sum, packing domains represent a new foundation to explore the interactions of chromatin and transcription at the single cell level in human health. Overall design: To investigate the relationship between higher order genome organization and terminal cellular differentiation, we took advantage of plastic myoblast cells and differentiated myotube cells. After treating 2 technical replicates of myoblasts with differentiation media, we generated Hi-C for each set of samples using the Qiagen Epitect Hi-C Kit (Qiagen, #59971). We processed each replicate using the HiC Nextflow pipeline and generated .cool files for each replicate. Replicates were merged to maximize resolution