Figures and data in How enzymatic activity is involved in chromatin organization

Version of Record: January 3, 2023
Accepted Manuscript: December 6, 2022

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Rakesh Das

Takahiro Sakaue

GV Shivashankar

Jacques Prost

Tetsuya Hiraiwa

(2022)
How enzymatic activity is involved in chromatin organization

eLife 11:e79901.

https://doi.org/10.7554/eLife.79901
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Figures
Tables
Additional files

5 figures, 1 table and 3 additional files

Figures

Figure 1

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Microphase separation of eu- and heterochromatic regions due to enzymatic activity.

(a) A random multiblock copolymer comprising A and B beads connected by springs confined within a spherical cavity. All the data are shown for block size $b = 4$ . (b) Topo-II enzyme catches two A’s in …

Figure 2

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Phase separation in system comprising self-avoiding and phantom regions.

(a) An equilibrium copolymer system comprising phantom (A′) and self-avoiding (B) beads is simulated in the absence of steric interaction between A′’s. The system shows microphase separation. A …

Figure 3 with 6 supplements

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Characteristics of Topo-II-induced microphase separation configurations.

(a) Density distribution of A and B beads in radial direction, plotted for fixed $ϵ_{H C} = 4$ . (b) Sample snapshots (hemisphere cuts) showing wall-like organization of A’s for $Λ > 0$ . (c) Local nematic order …

Figure 3—figure supplement 1

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AA bonds along the polymer are organized in planes of the walls formed by Topo-II.

We count the average number of AA and BB bonds (springs) along the polymer in local grids ( $ℓ \times ℓ \times ℓ$ in size) and calculate the amplitude of the nematic order parameter of those bonds. Negative, zero, and …

Figure 3—figure supplement 2

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Topo-II breaks local isotropy of the AA and BB bonds.

Phase diagrams indicating the mean local nematic order parameter of the AA and BB bonds (i.e., $S_{A A}$ and $S_{B B}$ ) are shown on the $Λ$ - $ϵ_{H C}$ plane for different composition of the system. $S_{A A} < 0$ and $S_{B B} > 0$ for $Λ > 0$ while …

Figure 3—figure supplement 3

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Comparison of monodisperse differential active model (MdDAM) with other transient models.

(a) Model schematic of Topo-II’s activity, and a sample snapshot is shown for $Λ = λ_{r a} (1 / λ_{a n} + 1 / λ_{n r}) = 0.0309$ in the absence of heterochromatin affinity. (**b–c**) Model schematics and sample snapshots are shown for two-state …

Figure 3—figure supplement 4

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A non-transient effective attraction model comparable to monodisperse differential active model (MdDAM) does not show phase separation.

To construct the effective model, we consider an additional potential $H_{A A} = \sum_{i, j \in A; r_{i j} \leq ℓ} h_{A A} = \sum_{i, j \in A; r_{i j} \leq ℓ} - ϵ_{A A} \exp (- α_{v e x} r_{i j}^{2})$ in Equation 2, and maintain all $h_{v e x}$ ’s in the repulsion state. MdDAM shows strong phase separation for the case with $ϕ_{A} = 0.5$ , $ϵ_{H C} = 0$ , …

Figure 3—figure supplement 5

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Effect of the geometry of the cavity on phase separation configurations.

We consider a cubic cavity of linear dimension $10 ℓ$ with closed boundary on z-direction. We assume periodic boundary condition for other two directions. We simulate monodisperse differential active …

Figure 3—figure supplement 6

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Features of heterochromatic foci shown for $ϵ_{H C} = 4$ .

Radius of gyration of segmented foci are plotted against their mean radial position $r_{f o c i, i} = (\sum_{B \in i} r_{B}) / n_{B, i}$ , $n_{B, i} \equiv$ number of B’s forming foci $i$ . A few sample foci have been shown on the respective panels. The images of …

Figure 4

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Microphase separation in bidisperse model, motivated from super-resolution microscopy data.

(a) Extracted data for mean cluster sizes and radial distribution functions of histone marks characteristic to eu- and heterochromatic regions. The data were extracted from Xu et al., 2018. …

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Tables

Table 1

Choice of model parameters.

Potential	Parameters
$H_{s p r i n g}$	$k = 22 e ℓ^{- 2}$ ; $r_{0} = \sum_{i \in c o n n e c t e d b e a d s} d_{i}$ .
$H_{v e x}$	Monodisperse model: $ϵ_{v e x} = 8 e$ ; $α_{v e x} = 7.9585 ℓ^{- 2}$ .
	Bidisperse model for AA pairs: $ϵ_{v e x} = 6.6539 e$ ; $α_{v e x} = 9.5686 ℓ^{- 2}$ .
	Bidisperse model for BB pairs: $ϵ_{v e x} = 11.507 e$ ; $α_{v e x} = 5.5330 ℓ^{- 2}$ .
	Bidisperse model for AB pairs: $ϵ_{v e x} = 8.9153 e$ ; $α_{v e x} = 7.1414 ℓ^{- 2}$ .
$H_{H C}$	$α_{H C} = 100 ℓ^{- 2}$ .
$H_{c o n f i n e m e n t}$	$p = 4 e$ ; $s = 2$ ; $R_{s} = 0.65 R_{g}$ ; $κ = 1 / R_{g}$ ; $R_{g} = d_{i} / 2$ where $i \equiv$ A, B

Additional files

Source code 1 CPU-based FORTRAN simulation code using OpenMP API. Instructions to use this can be found in the README text accompanying the source code.: https://cdn.elifesciences.org/articles/79901/elife-79901-code1-v2.zip
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Source code 2 CUDA FORTRAN simulation code using GPU acceleration. Instructions to use this can be found in the README text accompanying the source code.: https://cdn.elifesciences.org/articles/79901/elife-79901-code2-v2.zip
Download elife-79901-code2-v2.zip
Transparent reporting form: https://cdn.elifesciences.org/articles/79901/elife-79901-transrepform1-v2.pdf
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Figures

Microphase separation of eu- and heterochromatic regions due to enzymatic activity.

Phase separation in system comprising self-avoiding and phantom regions.

Characteristics of Topo-II-induced microphase separation configurations.

AA bonds along the polymer are organized in planes of the walls formed by Topo-II.

Topo-II breaks local isotropy of the AA and BB bonds.

Comparison of monodisperse differential active model (MdDAM) with other transient models.

A non-transient effective attraction model comparable to monodisperse differential active model (MdDAM) does not show phase separation.

Effect of the geometry of the cavity on phase separation configurations.

Features of heterochromatic foci shown for $ϵ_{H C} = 4$ .

Microphase separation in bidisperse model, motivated from super-resolution microscopy data.

Tables

Choice of model parameters.

Additional files

Source code 1

Source code 2

Transparent reporting form

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Microphase separation of eu- and heterochromatic regions due to enzymatic activity.

Phase separation in system comprising self-avoiding and phantom regions.

Characteristics of Topo-II-induced microphase separation configurations.

AA bonds along the polymer are organized in planes of the walls formed by Topo-II.

Topo-II breaks local isotropy of the AA and BB bonds.

Comparison of monodisperse differential active model (MdDAM) with other transient models.

A non-transient effective attraction model comparable to monodisperse differential active model (MdDAM) does not show phase separation.

Effect of the geometry of the cavity on phase separation configurations.

Features of heterochromatic foci shown for ϵH⁢C=4<math id="inf89"><mrow><msub><mi>ϵ</mi><mrow><mi>H</mi><mo>⁢</mo><mi>C</mi></mrow></msub><mo>=</mo><mn>4</mn></mrow></math>.

Microphase separation in bidisperse model, motivated from super-resolution microscopy data.

Choice of model parameters.

Source code 1

Source code 2

Transparent reporting form

Features of heterochromatic foci shown for $ϵ_{H C} = 4$ .