Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm [SLAM-seq]

Identity-specific interphase chromosome conformation must be re-established each time a cell divides. To understand how interphase folding is inherited, we developed an experimental approach that segregates chromosome-intrinsic factors from those inherited through the cytoplasm during the establishment of G1 nuclear architecture. Endogenous RanGAP1 or Nup93 proteins were degraded in pro-metaphase arrested DLD-1 cells to prevent the establishment of nucleo-cytoplasmic transport during mitotic exit and isolate the decondensing mitotic chromatin of G1 daughter cells from the cytoplasm. Using this approach, we uncovered a transient folding intermediate entirely driven by chromosome-intrinsic factors. In addition to conventional compartmental segregation, this chromosome-intrinsic folding program leads to prominent genome-scale microcompartmentalization of mitotically bookmarked and cell type-specific cis-regulatory elements. The microcompartment conformation is formed during telophase and subsequently modulated by a second folding program driven by factors inherited through the cytoplasm in G1. The nuclear import-dependent folding program includes cohesin and factors involved in transcription and RNA processing. The combined and inter-dependent action of chromosome-intrinsic and cytoplasmic inherited folding programs determines the interphase chromatin conformation as cells exit mitosis. Overall design: SLAM-seq profiling of total and nascent RNA in control or RanGAP1-depleted DLD-1 cells during mitosis. Time course experiment in which cells were labeled with 1mM 4-thio-uridine (4sU) in 1-hour, non-overlapping intervals comprising the final hour of culture for each time point. Unlabeled controls were included at pro-metaphase arrest (hour 0) and at the end of the 5-hour time course. Each experiment was performed in triplicate.