Reorganization of DNA loops by competition between condensin I and a linker histone

Abstract

Condensin-mediated loop extrusion is thought to be one of the primary mechanisms underlying mitotic chromosome assembly. However, how this process is affected by other chromosomal proteins, such as histones, is not well understood. Our previous study showed that in Xenopus egg extracts co-depleted of topoisomerase II and the histone chaperone Asf1, a highly characteristic chromatin structure called the "sparkler" is assembled. The sparkler is a compact structure assembled on nucleosome-free, entangled DNA in which multiple protrusions radiate from a core. Interestingly, condensin I is concentrated at the tips of the protrusions, whereas the linker histone H1.8 is enriched in the remaining regions of the structure. To understand the biophysical mechanisms underlying sparkler assembly, we construct a model predicting that DNA loops extruded from the entangled DNA undergo phase separation into two domains: loops enriched in condensin I remain as protrusions, whereas those enriched in H1.8 are reeled into the central region. We propose that H1.8 competes with condensin I for DNA binding, thereby reorganizing DNA loops formed by condensin I under this specialized condition.