Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe

Abstract

The question of how self-interacting chromatin domains in interphase chromosomes are structured and generated dominates current discussions on eukaryotic chromosomes. Numerical simulations using standard polymer models have been helpful in testing the validity of various models of chromosome organization. Experimental contact maps can be compared with simulated contact maps and thus verify how good is the model. With increasing resolution of experimental contact maps, it became apparent though that active processes need to be introduced into models to recapitulate the experimental data. Since transcribing RNA polymerases are very strong molecular motors that induce axial rotation of transcribed DNA, we present here models that include such rotational motors. We also include into our models swivels and sites for intersegmental passages that account for action of DNA topoisomerases releasing torsional stress. Using these elements in our models, we show that transcription-induced supercoiling generated in the regions with divergent-transcription and supercoiling relaxation occurring between these regions are sufficient to explain formation of self-interacting chromatin domains in chromosomes of fission yeast (S. pombe).

Figure 1.

Simulations of effects of divergent transcription in a small chromatin loop in which positive supercoiling generated ahead of RNA polymerases is dissipated. (A–C) Simulation snapshots showing gradual accumulation of negative supercoiling. The starting configuration is shown in A. The arrowhead-shaped objects indicate positions of torsional motors that mimic the effect of RNA polymerases by generating torque and inducing local axial rotation of the chain. The modelled chain reflects the properties of semi-flexible polymers like DNA or chromatin fibres with bending and torsional resistance. Only in the short region between the two torsional motors the chain has no torsional resistance. The region with no torsional resistance (swivel) is graphically presented as a sharp tip contacting a flat surface to resemble a tip of a spinning top that is in a contact with the supporting surface but is free to rotate. (D) The magnitude of writhe (one of the measures of supercoiling (32)) increases and then saturates with time (the writhe in negatively supercoiled DNA and chromatin fibres is negative).

Figure 2.

Simulations of large chromosome fragments with 10 divergent transcription domains separated by sites where torsional stress gets dissipated and zones where portions of modelled chains can pass through each other. (A) Simulation snapshot. Each domain with divergent transcription is marked with a different colour. Torsional motors and swivel sites are presented as in Figure 1A–C. The zones where portions of the chain can pass through each other are presented as semi-transparent. (B) Schematic linear map of two consecutive domains showing the location of modelled RNA polymerases with TOP1 preceding them and also showing location of zones of passages. Circular arrows indicate the direction of rotation induced by respective polymerases. Normal arrows indicate the direction of transcription. (C) Contact map obtained upon analysis of nearly 20 millions of configurations of modelled chromosome fragments such as shown in A. Notice that each of the modelled divergent transcription domains forms a TAD-like region with increased frequency of internal contacts. The blue horizontal and vertical lines indicate positions of gene convergence imposed in our model. (D) Experimental contact map of a portion of S. pombe chromosome with 10 divergent transcription domains. This contact map was obtained using experimental data deposited by Mizuguchi et al. (11) and corresponds to the portion of chromosome 2 ranging from ∼750 to 1300 kb positions of that chromosome. The blue horizontal and vertical lines indicate positions of local maxima of gene convergence in the corresponding chromosome fragment as determined by Mizuguchi et al. (11). Notice that the sizes of self-interacting domains in the modelled chromosome fragment (A and C), reflect the distribution of self-interacting domain sizes observed in all S. pombe chromosomes and were not adjusted to fit the sizes of self-interacting domains in the chromosome fragment, whose contact map is shown in C.

Figure 3.

Homeostatic control of supercoiling. (A) Evolution of writhe in one domain (highlighted in blue) within thermally equilibrated chromosome fragment with 10 domains. The snapshot of the entire chromosome fragment is taken at the beginning of the simulation interval for which the writhe profile is shown. After about 25 simulation steps during which writhe was changing moderately there was a simulation step time during which writhe has changed by ∼2. Such a change is an indication of an intersegmental passage. (B–D) Snapshots of the zone of passage (encircled in A), showing the progress of one intersegmental passage. Simulation time steps corresponding to these snapshots are indicated with arrows in the writhe profile. The writhe profile shows that after the initial drop of the magnitude of writhe after the passage, the writhe values tend to return to the level before the passage.

Figure 4.

Simulations testing the cohesin barrier model. (A) Snapshot from the simulation of chromatin fibres with encircling cohesin rings maintained at regular intervals. (B and C) Contact maps obtained for a large statistical sample of equilibrated configurations such as shown in A. In B, the applied colour scale is linear as the one used in the experimental contact maps of Mizuguchi et al. (11) and in the simulated contact maps presented in Figure 2. In C, the applied colour scale is logarithmic. Notice that the presence of localized cohesin rings results in a local depletion of contacts at chromatin portions shielded by the rings, but does not result in formation of characteristic triangles indicating presence of self-interacting domains. The arrows indicate lines with depleted contacts.