A role for condensin-mediator interaction in mitotic chromosomal organization [PRO-Seq]

Eukaryotic genomes are organized into layers of chromatin domains, such as topologically associating domains (TADs) and A/B compartments. TADs (i.e., cohesin-mediated chromatin domains) are restricted by CCCTC-binding factor (CTCF) and convergent genes in higher eukaryotes and fission yeast, respectively. However, molecular mechanisms underlying the formation of condensin-mediated chromatin domains remain largely unclear. Here, we investigate the role of newly identified interaction between the Cnd1 condensin and Pmc4 mediator subunits. We develop a condensin mutation, cnd1-K658E, that impairs the condensin-mediator interaction and find that this mutation diminishes condensin-mediated domains and causes defects in chromosomal segregation. The condensin-mediator interaction is involved in recruiting condensin to highly transcribed genes and mitotically activated genes, the latter of which demarcate condensin-mediated domains. Our study also predicted that the condensin-mediator interaction and its function in chromosomal segregation are potentially conserved in human cells. This study provides a novel insight into how genome-wide gene expression is connected to the mitotic chromosomal architecture via the condensin-mediator interaction. Overall design: Nascent RNA profiles in the following conditions were determined by PRO-seq. The endogenous Cnd1 expression was repressed by culturing cells in EMM medium containing thiamine and auxin, and the exogenous Cnd1 proteins (WT and K658E) were provided from the plasmids. For Pmc4 depletion, the endogenous Pmc4 was degraded by the AID system, and the exogenous Pmc4 protein was provided from the plasmid (Pmc4 WT).