Active Transcription Regulates Mesoscale Genomic Organization via Active Extrusion of Chromatin Loops

Transcriptional activity has recently been shown to increase the DNA supercoiling accelerating the formation of transcriptionally active DNA loops, and hence potentially dictating chromatin spatial organization. However, the quantitative role that transcription and epigenetic regulation synergistically play in genome-wide chromatin organization is yet unknown. We present a mesoscale phase-field model to explain the underlying physics of nuclear chromatin organization in presence of DNA looping. We capture the chromatin-lamina and chromatin self-interaction energetics and the kinetics of the diffusion of nucleoplasm and epigenetic marks. In addition, methylation and acetylation reactions drive a non-conservative interconversion of the euchromatin (EC) and heterochromatin (HC) phases. DNA loop extrusion is captured via a kinetic conversion of HC into EC in RNAPII-rich regions. Our analysis predicts that at steady state HC domain size is governed solely by the kinetics of acetylation, methylation, and DNA loop extrusion. Our simulations, with super-resolution H2B imaging of in-vitro nuclei, reveal that the transcription abrogation increases HC domain sizes. We predict that enhanced DNA looping results in smaller HC domains – validated by super-resolution imaging of WAPL-deficient nuclei. Lastly, we predict the joint effects of WAPL deficiency and transcription 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.