Fig. 1: RCMC deeply resolves 3D genomic architecture at the M-to-G1 transition.
From: Dynamics of microcompartment formation at the mitosis-to-G1 transition
a, Overview of the experimental system. As previously described18, G1E-ER4 cells with an mCherry-tagged mitotic domain reporter are PM-arrested using nocodazole and flow-sorted after release to capture highly pure cell populations across five M-to-G1 time points: PM (no release), AT (25 min after release), EG1 (1 h), MG1 (2 h) and LG1 (4 h) (Extended Data Fig. 1a). The RCMC protocol28 is applied to each of these cell populations; briefly, chromatin is chemically fixed, digested with micrococcal nuclease (MNase) and biotin-labeled before proximity ligation joins spatially proximal fragments. After enrichment for ligated interactions, fragments are library-prepped, amplified and region-captured to create an RCMC library that is sequenced, mapped and normalized to create contact matrices. b, Schematic representation of how A/B compartments, TADs, CTCF loops, E–P loops and microcompartments appear in contact maps across scales. c, Interaction probability curves comparing the interaction frequency at different genomic separations (s) for the five RCMC datasets. The first derivative of these P(s) curves is shown at the bottom. d, The 3C data density in captured regions for RCMC versus Hi-C data from Zhang et al.18. Averaged counts for the number of unique reads across five captured regions are plotted for increasing interaction distances for all datasets at a 250-bp bin size.
