Random sub-diffusion and capture of genes by the nuclear pore reduces dynamics and coordinates inter-chromosomal movement
- Department of Molecular Biosciences, Northwestern University, United States
- Department of Physics, Harvard University, United States
Figures
Figure 1
Continuous and dynamic positioning at the nuclear periphery.
(A) Representative confocal micrographs of cells having the LacO array integrated at a locus of interest, expressing GFP-LacI and Pho88-mCherry (Robinett et al., 1996; Brickner and Walter, 2004; Bric…
Figure 2 with 1 supplement
Mean-squared displacement (MSD) of chromatin sub-diffusion.
(A) Schematic of fluorescent foci within the yeast cell. Fluorescently tagged spindle pole body (SPB), cytoplasmic µNS, and chromosomal locus were tracked over 200 × 200 ms. Example micrographs of …
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Figure 2—source data 1
Comma-separated tables of tracking data used for Figure 2B, D, E, and F.
- https://cdn.elifesciences.org/articles/66238/elife-66238-fig2-data1-v2.zip
Figure 2—figure supplement 1
MSD of peripheral vs nucleoplasmic cells.
To monitor peripheral localization during particle tracking for MSD, we developed an automated tracking system in R that uses the imageR package to threshold, denoise, and detect both the nuclear …
Figure 3
Interaction with the NPC reduces chromatin sub-diffusion.
(A–F) MSD of URA3 (A–D) and INO1 (E, F) in strains grown in the indicated media. Dark line indicates average MSD, ribbon = bootstrapped SEM. Insets: peripheral localization of each locus (mean % of …
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Figure 3—source data 1
Comma-separated tables of tracking data used for Figure 3.
- https://cdn.elifesciences.org/articles/66238/elife-66238-fig3-data1-v2.zip
Figure 4 with 2 supplements
A fractional Brownian motion simulation of chromatin sub-diffusion.
(A, C) Randomly selected example paths over 5 min at 200 ms time resolution. Color scale represents time. Paths were simulated using parameters (diffusion coefficient and anomalous exponent) …
Figure 4—figure supplement 1
Comparison of simulations of sub-diffusion of nucleoplasmic chromatin.
Four different simulations of chromatin diffusion were compared with URA3 for MSD (A, B) or nuclear position (C, D). The uniform simulation generated uniformly distributed step sizes in the x and y …
Figure 4—figure supplement 2
Optimization of binding probability and retention probability by comparison with URA3:GRS1.
The probability of binding and the probability of retention were independently varied and compared with the behavior of URA3:GRS1. (A, B) Χ2 sum of differences between mean MSD plots of URA3:GRS1 …
Figure 5 with 1 supplement
Repositioning from the nucleoplasm to the NPC.
(A) Simulated repositioning. Simulated paths, using either the fractional Brownian simulation or the simulation+zip code, were initiated at random positions within 2 µm diameter nucleus and followed …
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Figure 5—source data 1
Comma-separated tables of simulated paths and tracking data used for Figure 5.
- https://cdn.elifesciences.org/articles/66238/elife-66238-fig5-data1-v2.zip
Figure 5—figure supplement 1
Loss of Myo3 delays GRS1-dependent repositioning to the nuclear periphery.
The URA3:INO1 locus (having GRS1 but not GRS2) tagged with the LacO array shows GRS1-dependent localization to the nuclear periphery upon activation (Ahmed et al., 2010). (A) Wild-type, myo5∆, and my…
Figure 6
Dynamics of inter-chromosomal clustering.
(A) Confocal micrographs of diploid cells with two loci marked with LacO arrays, expressing LacI-GFP and Pho88-mCherry. Distance between LacO arrays was measured over 200 × 200 ms time points in …
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Figure 6—source data 1
Comma-separated tables of simulated paths and tracking data used for Figures 6 and 7.
- https://cdn.elifesciences.org/articles/66238/elife-66238-fig6-data1-v2.zip
Figure 7 with 1 supplement
Inter-chromosomal clustering leads to coordinated movement.
(A) Workflow for tracking and analyzing movement of LacO array pairs. For each step from a time series, step distance and step angle are measured (top) and the difference in angles computed …
Figure 7—figure supplement 1
Dynamic coordination analysis of URA3.
Diploid strains having the LacO array integrated at both alleles of URA3 were grown in SDC ± histidine; the loci were tracked and analyzed for correlated step size and step angle as described for Fig…
Author response image 1
Additional files
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Supplementary file 1
Mean squared displacement parameters.
- https://cdn.elifesciences.org/articles/66238/elife-66238-supp1-v2.docx
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Supplementary file 2
Strains used in this study.
- https://cdn.elifesciences.org/articles/66238/elife-66238-supp2-v2.docx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/66238/elife-66238-transrepform-v2.docx
