Mesoscale chromatin organization is regulated by active transcription and epigenetic regulation.

Abstract

Epigenetically regulated post-translational modifications of histone tails via acetylation or methylation have been established to play a role in determining the transcriptional status of genes. Beyond epigenetic regulation, chromatin loop extrusion through cohesin rings, driven by transcription-generated DNA supercoiling, can also alter spatial chromatin organization. Here, we present a mesoscale phase-field model to explain the underlying physics of chromatin reorganization in the presence of transcriptionally driven chromatin loop extrusion. The model incorporates energetic considerations of chromatin-chromatin and chromatin-lamina interactions leading to phase separation in the interior and periphery of the nucleus. We incorporate the kinetics of the diffusion of nucleoplasm and epigenetic marks. In addition, a non-conservative interconversion of euchromatin and heterochromatin is captured by incorporating first-order reaction kinetics of histone methylation and acetylation. Lastly, and vitally, the extrusion of genetically expressive chromatin enhancer-promoter loops is included via a kinetic conversion of heterochromatin into euchromatin in the presence of RNAPII-mediated transcriptional activity. Our theoretical analysis predicts that the size of the stable heterochromatin domains is determined solely by the kinetics of acetylation, methylation, and chromatin loop extrusion. Our numerical simulations, in conjunction with the super-resolution in-vitro nucleus imaging techniques, reveal that the absence of transcription increases chromatin compaction and heterochromatin domain sizes in the nucleus's interior and periphery. We also predict that enhanced chromatin loop extrusion would result in reduced sizes of heterochromatin domains - which is validated by super-resolution imaging of WAPL-deficient nuclei. Lastly, we reveal the synergistic effects of WAPL deficiency and transcriptional abrogation such that chromatin decompaction in WAPL-deficient nuclei is blocked by inhibiting transcription. By uncovering the physical mechanisms of mesoscale chromatin organization in the nucleus, our model presents a new step in understanding how cell fate is affected by its chemo-mechanical environment.