The length and strength of compartmental interactions are modulated by condensin II activity [Hi-C]

Condensin II plays a crucial role in shaping chromosome structure throughout the cell cycle, but its specific functions during interphase have remained unclear. In this study, we utilized Oligopaints and Hi-C techniques to investigate how changes in condensin II levels affect chromosome organization across various length scales. Our findings reveal that condensin II has a significant impact on long-range interactions within chromosomes, which are essential for the organization of intrachromosomal compartments. Importantly, these effects occur independently of the chromatin state. Furthermore, overexpression of condensin II during interphase leads to the formation of "peri-centric super stripes" observed through Hi-C analysis, indicating a disruption of the boundary between heterochromatin and euchromatin on Drosophila chromosomes. Collectively, our results challenge the existing belief that compartments form without the involvement of a loop extruder and suggest that condensin II activity is a prerequisite for driving proximity between distal compartmental domains within chromosomes. Overall design: To investigate the consequences of condensin II depletion on gene expression, we depleted the condensin II subunit Cap-H2 in the Drosophila BG3 cell line. We performed RNA-sequencing in Cap-H2 knockdown and control (Brown knockdown) cells. ***Please note that all sample records (including their raw and processed data files) have been updated on Feb 12, 2024.