Dynamics of microcompartment formation at the mitosis-to-G1 transition

As cells exit mitosis and enter G1, mitotic chromosomes decompact and transcription is reestablished, with prior studies showing that essentially all interphase 3D genome features including A/B-compartments, TADs, and CTCF loops are lost during mitosis. Microcompartments, nested focal interactions between cis-regulatory elements (CREs), can now be resolved using Region Capture Micro-C (RCMC), though the dynamics of their formation remain unknown. We therefore applied Region Capture Micro-C to G1E-ER4 cells across five mitosis-to-G1 stages: prometaphase, ana/telophase, early G1, mid G1, and late G1, along with an asynchronous condition. Five mouse loci ranging from 1-2 Mb in size were selected for capture: Id1, Klf1, Cdt1, Dag1, and Myc. Follow-up RCMC experiments were also performed at these loci in an SMC2 (condensin) degron G1E-ER4 subline, in which cells were arrested in prometaphase and auxin-treated for five tested depletion conditions: 0h, 0.5h, 1h, 4h, and 8h. We find that microcompartments form early in the M-to-G1 transition but weaken as cells enter G1, suggesting that microcompartmentalization is distinct from A/B-compartmentalization and loop extrusion. Region Capture Micro-C was performed in G1E-ER4 cells arrested to different stages of the mitosis-to-G1 transition and varying degrees of condensin depletion