Cohesin and condensin extrude DNA loops in a cell cycle-dependent manner.

Stefan Golfier,Jan Brugués,Hiroshi Kimura,Thomas Quail

doi:10.7554/elife.53885

Abstract

Loop extrusion by structural maintenance of chromosomes (SMC) complexes has been proposed as a mechanism to organize chromatin in interphase and metaphase. However, the requirements for chromatin organization in these cell cycle phases are different, and it is unknown whether loop extrusion dynamics and the complexes that extrude DNA also differ. Here, we used Xenopus egg extracts to reconstitute and image loop extrusion of single DNA molecules during the cell cycle. We show that loops form in both metaphase and interphase, but with distinct dynamic properties. Condensin extrudes DNA loops non-symmetrically in metaphase, whereas cohesin extrudes loops symmetrically in interphase. Our data show that loop extrusion is a general mechanism underlying DNA organization, with dynamic and structural properties that are biochemically regulated during the cell cycle.

Highlights

Chromatin undergoes a dramatic reorganization during the cell cycle (Hirano and Mitchison, 1991; Rowley and Corces, 2018; Nagano et al, 2017)
In mock-depleted extracts, loops formed but at a much lower frequency (Figure 1—figure supplement 1D and Figure 1—video 10) and seemed to compete with nucleosomes for available DNA slack. These results show that DNA loop extrusion can be reconstituted in Xenopus egg extracts in metaphase and interphase
Our findings provide the first direct evidence that loop extrusion is a general mechanism of DNA organization in a cellular context, and, that it is differentially regulated during the cell cycle

Summary

Introduction

Chromatin undergoes a dramatic reorganization during the cell cycle (Hirano and Mitchison, 1991; Rowley and Corces, 2018; Nagano et al, 2017). Chromosomes undergo large-scale compaction, leading to the loss of specific boundaries and the shutdown of transcription, which is achieved by arranging chromatin into an array of condensed loops (Marsden and Laemmli, 1979; Earnshaw and Laemmli, 1983; Naumova et al, 2013; Goloborodko et al, 2016; Uhlmann, 2016; Kinoshita and Hirano, 2017) These different degrees of organization require the coordinated activity of protein complexes such as structural maintenance of chromosomes (SMCs) proteins (Nasmyth, 2001; Yatskevich et al, 2019; Fudenberg et al, 2016; Nuebler et al, 2018; Hirano et al, 1997; Bouwman and de Laat, 2015), but how these complexes organize chromatin dynamically during the cell cycle is still unknown.

Methods

Results

Conclusion