RotoStep: A Chromosome Dynamics Simulator Reveals Mechanisms of Loop Extrusion

Abstract

ChromoShake is a three-dimensional simulator designed to explore the range of configurational states a chromosome can adopt based on thermodynamic fluctuations of the polymer chain. Here, we refine ChromoShake to generate dynamic simulations of a DNA-based motor protein such as condensin walking along the chromatin substrate. We model walking as a rotation of DNAbinding heat-repeat proteins around one another. The simulation is applied to several configurations of DNA to reveal the consequences of mechanical stepping on taut chromatin under tension versus loop extrusion on single-tethered, floppy chromatin substrates. These simulations provide testable hypotheses for condensin and other DNA-based motors functioning along interphase chromosomes. Our model reveals a novel mechanism for condensin enrichment in the pericentromeric region of mitotic chromosomes. Increased condensin dwell time at centromeres results in a high density of pericentric loops that in turn provide substrate for additional condensin.There has been a revolution in understanding the higher-order structure and organization of chromosome in the past decade. Several major approaches (3C, ChromEMT, and super-resolution microscopy) are indicative of a disordered array of loopy fibers that emanate from an axial core (Dostie and Bickmore 2012;Dekker et al. 2013;Ou et al. 2017). The hierarchical models of structural intermediates building from 11 to 30 nm and larger fibers are not borne out in these recent 3D and live-cell studies (Ou et al. 2017). DNA looping was first observed in squash preparations of salamander eggs under the light microscope by the embryologist Oskar Hertwig in the early 1900s (Hertwig 1906). Paulson and Laemmli (1977) observed DNA loops when examining chromosome spreads in isolated mammalian cells. In metaphase, the loops emanate from a protein-rich chromosome scaffold. The chromosome scaffold is enriched in topology-adjusting proteins, such as topoisomerase II and the SMC (structural maintenance of chromosomes) proteins, known as condensin (Earnshaw et al. 1985;Hirano 2006).Loops are a natural consequence of the entropic fluctuations and excluded volume interactions of tethered polymer chains in a confined space, such as the nucleus (Vasquez et al. 2016). If we consider the genome as a ball of yarn, the formation of loops can be appreciated as chains that randomly collide and wiggle around one another. Energy-requiring processes are also involved in loop formation. The earliest suggestion of loop extrusion came from the trombone model of DNA replication (Sinha et al. 1980;Alberts et al. 1983) and direct visualization of DNA looping at the replication fork (Park et al. 1998). More recently, SMC proteins (e.g., cohesin and condensin), which bind and hydrolyze ATP, have been cited as having loop extrusion potential (Alipour and Marko 2012). Condensin has garnered attention based on recent studies showing it to be a DNA translocase (Terekawa et al. 2017).Condensin is composed of five subunits, two coiledcoils SMC2 and 4, a kleisin ...

Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold

“…Single-molecule experiments have indeed observed DNA translocation (Terakawa et al, 2017) and loop-extrusion (Ganji et al, 2018) dynamics for yeast condensin, supporting this model. A possible molecular mechanism underlying loop extrusion by condensin which is consistent with the observations of (Ganji et al, 2018) has been presented in (Lawrimore et al, 2017). …”

Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold

“…Single-molecule experiments have indeed observed DNA translocation (Terakawa et al, 2017) and loop-extrusion (Ganji et al, 2018) dynamics for yeast condensin, supporting this model. A possible molecular mechanism underlying loop extrusion by condensin which is consistent with the observations of (Ganji et al, 2018) has been presented in (Lawrimore et al, 2017).…”

Condensins and cohesins – one of these things is not like the other!

“…Biophysical studies focused on the impact of DNA as a floppy substrate, and explored the effect of replacing a tautly anchored DNA substrate for a floppy one. The resulting simulations succeeded in generating models in which condensin extrudes DNA loops (Fudenberg et al, 2016;Lawrimore et al, 2016Lawrimore et al, , 2017. Consistent with this revelation, a tour de force of imaging provided new evidence that condensin migration is coupled to asymmetric loop extrusion (Ganji et al, 2018).…”

“…Intriguingly, the distance between condensin and one of the DNA-surface anchor points remained fixed, whereas the distance between condensin and the opposing DNA-surface anchor point decreased. This suggests that one domain of condensin binds to and anchors itself to DNA, whereas a separate condensin domain actively drives migration along DNA and, concomitantly, loop extrusion (Lawrimore et al, 2017;Ganji et al, 2018). Whether unidirectional condensin translocation arises from discriminating between Watson/Crick strand polarities within the DNA duplex remains an intriguing possibility.…”

“…In the absence of imposed architecture (nucleosomes, chromatin remodelers, SMC complexes, etc. ), condensin could bind any proximal segment of a floppy, wriggling DNA and in a non-directed fashion (Fudenberg et al, 2016;Lawrimore et al, 2016Lawrimore et al, , 2017. This model, however, does not easily lend itself to explain unidirectional motion or accommodate the tension that is likely generated on DNA during condensation.…”