Global chromatin mobility induced by a DSB is dictated by chromosomal conformation and defines the HR outcome

6 figures and 4 additional files

Figures

Figure 1 with 1 supplement
Tracks homologous recombination in vivo (THRIV), a system to follow homologous recombination (HR) in vivo.

(A) Schematic representation of the two sequences used to track recombination events during time. The recipient mCherry-I-SceI has a 30pb I-SceI sequence followed by a stop codon (red bar) inserted at 57 amino acids from the end of the mCherry coding sequence. The donor (dCen) is a full-length mCherry lacking promoter and terminator sequences, carried on a centromeric plasmid. A functional mCherry could be expressed only after HR. (B) Schematic 2D representation of the Rabl spatial configuration of two chromosomes in the nucleus of Saccharomyces cerevisiae. The spindle pole body (rectangle), the microtubules (lines), and the centromeres (spheres) are in yellow. Telomeres are shown as gray/black spheres attached to the nuclear envelope. An orange circle represents the dCen plasmid. The gray crescent symbolizes the nucleolus. Lightening symbolize the targeted I-SceI cutting sites (cs) on chromosome IVR arm, with same color code as in the linear representation represented below. The cs are respectively located at 5 kb from centromere CEN IV (red, strain C), 400 kb from CEN IV (green, strain L), and 20 kb from telomere TEL IVR (blue, strain S), distances are in kb The green dot visualizes the locus used to monitor mobility on undamaged chromosome VR. (C) I-SceI cleavage efficiency is measured in a non-donor strain by qPCR using primers flanking the I-SceI cs. The error bars represent the standard deviation of five or two independent experiments for strain C and strains L, S, respectively. (D) FACS analysis of the cell cycle of strains C, L, and S after induction of I-SceI with or without dCen plasmid. For the quantification of the cell cycle progression, the amount of DNA is measured with Sytox after fixation with ethanol and treatment with RNase. The peaks corresponding to 1n and 2n amount of DNA are indicated. (E) Drop assay (10-fold serial dilutions) showing the sensitivity of C, L, and S strains, containing a plasmid expressing or not I-SceI (-DSB, +DSB, respectively), with dCen plasmid or without (empty plasmid), when I-SceI is induced for 48 hr (galactose) or not (raffinose). (F) HR kinetics upon induction of I-SceI in the presence of dCen in C, L, or S strains. Percentages of repaired red cells were measured by FACS after PFA fixation in the absence of Sytox. Error bars represent the standard deviation of three independent experiments, five independent experiments for strain C. Mann-Whitney test, n.s., non-significant.

Figure 1—figure supplement 1
Validation of the THRIV system.

(A) Growth curve of strains C (red), L (green), and S (blue) showing a similar doubling time. The error bars represent the standard deviation of three independent experiments. (B) I-SceI induction ratio measured by transcription quantitative reverse PCR (RT-qPCR) using primers hybridizing into the I-SceI coding sequence. The error bars represent the standard deviation of three independent experiments, except for 6 hr done two times. (C) Quantification of red and white cells in strains C and S, 48 hr after I-SceI induction on galactose plates before DNA extraction and PCR amplification around the I-SceI cut site (cs) of those strains. The error bars represent the standard deviation of two independent experiments, the total amount of counted cells was around 200/experiment. If the recipient I-SceI cs containing sequence is fully repaired by homologous recombination with the donor dCen plasmid, it cannot be cut by I-SceI in vitro. pGPS2 I-SceI cs containing plasmid is used as a control for in vitro digestion. (D) Boxplot of 2D distances measured in μm between the spindle pole body (SPB) (SPC29-mCherry, red) and dCen plasmid containing tetO repeats, labeled in green (TetR-GFP). As references, chromosome loci labeled either close to the centromere (YDR003w, 5 kb from CenIV) or the telomere (YER188C, 8 kb from TELVR) are shown. Between n=169, 3520 and 3461 cells were analyzed for each strain in three independent experiments. Brackets indicate the result of a rank-sum test between distributions, with ‘n.s.’ for ‘not significant’ (p>0.05) and *** for p<10–3. Below, examples of cell nuclei with the two red and green labeled loci allowing calculation of the SPB-loci distances. As expected, the donor sequence dCen on the centromeric plasmid is located close to the SPB, the subtelomeric sequence far from it, see Therizols et al., 2010.

Figure 1—figure supplement 1—source data 1

DO values for growth curve.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig1-figsupp1-data1-v1.zip
Figure 1—figure supplement 1—source data 2

Transcription quantitative reverse PCR (RT-qPCR) values for I-SceI expression.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig1-figsupp1-data2-v1.zip
Figure 1—figure supplement 1—source data 3

Red cells values after I-SceI induction.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig1-figsupp1-data3-v1.zip
Figure 1—figure supplement 1—source data 4

Agarose gel after PCR amplification of the I-SceI cutting site and cut by I-SceI in vitro.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig1-figsupp1-data4-v1.zip
Figure 1—figure supplement 1—source data 5

2D distances values.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig1-figsupp1-data5-v1.zip
Figure 2 with 1 supplement
Enhanced global chromatin dynamics after damage is dictated by double-strand break (DSB) and donor positions.

(A) As in Figures 1B and 2D and linear schematics of the undamaged chromosome containing the visualization of the locus on chromosome V (V-Vis) locus used for global mobility tracking, indicated as (tracked). V-Vis consists of TetO repeats bound by the TetR repressor protein fused to the fluorescent protein GFP, integrated into the MAK10 locus on the left arm of chromosome V at 98 kb from the centromere CENV (green dot). (B) Mean squared displacements (MSDs) as a function of time for the V-Vis locus in strain C (red), L (green), and S (blue) respectively after 6 hr in galactose medium in the absence or the presence of I-SceI expressing plasmid (-DSB, +DSB) and in the presence of the donor plasmid (-DSB+dCen, +DSB+dCen plasmid), or the empty plasmid (-DSB, +DSB). MSDs are calculated from video microscopy data with a time sampling of ∆t=100 ms. Between n=405 and n=1794 cells were analyzed for each strain in six independent experiments. The exact number of cells analyzed to calculate each curve (n) is indicated in supplementary file 1. The gray curve corresponds to the average MSD of the strain C without DSB in the presence of dCen or of the empty plasmid. (C) The global increase in dynamics after 6 hr in galactose medium is verified for (i) another pericentromeric DSB (left); (ii) other tracked loci (middle), and (iii) donor sequences distinct than dCen plasmid (right). (i) I-SceI cut site (cs) is inserted at 8 kb from CENII (red curve; n=209), MSD without DSB induction is shown in gray (n=356). Four independent experiments were done. (ii) MSDs are calculated by tracking TetO repeats inserted on chromosome XIII at 340 and 650 kb of the centromere (red and pink curves, n=594 and n=1085, respectively) upon induction of I-SceI DSB on peri-centromere of chromosome IV. The gray curves correspond to the average MSDs without induction for both strains (n=2582 and n=1076, respectively). Seven independent experiments were done; (iii) the donor sequence is inserted on chromosome VII (dChr.VII) after a DSB in subtelomeric position (S, blue lightening). MSDs are measured after insertion of donor sequence at 5 or 300 kb of CEN VII (dark and light blue, n=1403 and n=1496, respectively). -DSB curves represent MSDs when DSB is not induced (n=900 and n=895, respectively). Seven independent experiments were done. 2D schemes of Rabl chromosome conformation with positions of the DSB, the tracked locus, or the donor sequences are shown on the top of each MSD graph as in Figure 1B.

Figure 2—figure supplement 1
Mean square displacements (MSD) at 10s of V-Vis after a single DSB.

(A) Mean squared displacements (MSDs) of strains C (red), L (green), and S (blue), respectively, after 6 hr in galactose medium in the absence of donor sequence at long time points (n=1172; n=1390; n=608, respectively). The gray curve corresponds to the average MSDs without induction for the C strain (n=1243). Three independent experiments were done. (B) Gradual increase of MSD with induction time in the strain C in the absence of donor. The relative ratio of MSDs at 10 s (+DSB/-DSB) for each time point after induction of I-SceI are shown. Values of MSD at 10 s and number of cells analyzed to calculate the chart is indicated in supplementary file 1. (C) Boxplots of the distribution of MSDs at 10 s from Figure 2B for strains C, L, and S with the same color code. Median values, lower and upper quartiles are shown. Whiskers indicate the full range of measured values, except for outliers represented by small red dots. Parentheses indicate the result of a Wilcoxon rank-sum test between distributions, with the p-value. n.s., non significant, * (p<0.05), ** (p<0.001), *** (p<0.0001).

Figure 2—figure supplement 1—source data 1

Mean squared displacement (MSD) values.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig2-figsupp1-data1-v1.zip
Figure 2—figure supplement 1—source data 2

Values of mean squared displacement (MSD) at 10 s for different time points of I-SceI induction.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig2-figsupp1-data2-v1.zip
Figure 2—figure supplement 1—source data 3

Values of mean squared displacement (MSD) at 10 s.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig2-figsupp1-data3-v1.zip
Figure 3 with 1 supplement
Proximal mobility is Rad9 independent.

(A) Non-repaired cells (white cells, n=584) show increased global mobility, while repaired cells (red cells, n=519) recover normal global mobility. Mean squared displacements (MSDs) of the visualization of the locus on chromosome V (V-Vis) locus in strain C as a function of time, calculated as in Figure 2A. The gray and red curves correspond respectively to strain C in the presence of the donor dCen plasmid after 12 hr in galactose medium with a plasmid not expressing I-SceI (-DSB) and expressing I-SceI (+DSB). MSDs are calculated after color visual cell sorting. Red MSD full curve corresponds to cycling red cells, red empty curve corresponds to white G2/M arrested cells. Examples of white, G2/M arrested and red, cycling cells are shown. Bar scale, 2 µm. Seven independent experiments were done. (B) Box plots of MSDs at 10 s of undamaged, white and red cells 12 hr after I-SceI induction. The color code corresponds to that used in (A). (C) MSDs in strains C and S in wild-type (WT) and Δrad9 mutant. MSDs are calculated as in Figure 2 upon 6 hr of double-strand break (DSB) induction with empty plasmid or with dCen plasmid (+DSB: n=380 [C strain], n=103 [S strain], and +DSB+dCen: n=452 [C strain], n=98 [S strain], respectively). Controls without DSB are also shown (-DSB: n=590 [C strain], n=176 [S strain]). (D) Homologous recombination (HR) kinetics upon induction of I-SceI in the presence of dCen in WT (black) and Δrad9 (orange) C or S strains were measured by FACS as in Figure 1F. Error bars represent the standard deviation of three independent experiments.

Figure 3—figure supplement 1
Implication of Rad9 in survival, cell cycle and global dynamics.

(A) Scatter plot showing the mean squared displacement (MSD) at 10 s of the damaged-only population (in white), the repaired-only population (in red), or the 20–80% mixed population (in gray) 6 or 12 hr after double-strand break (DSB) induction.( B) I-SceI cleavage efficiency measured in Δrad9 mutant by qPCR using primers flanking the I-SceI cut site (cs). The error bars represent the standard deviation of three independent experiments. (C) Left: Analysis of the cell cycle of Δrad9 C and S strains after induction of I-SceI with dCen. Quantification is done as in Figure 1D. The peaks corresponding to 1n and 2n amount of DNA are indicated. Right: Drop assay (10-fold serial dilutions) showing the sensitivity of wild-type (WT) and Δrad9 C or S strains, containing a plasmid expressing or not I-SceI (-DSB, +DSB respectively), with dCen or an empty plasmid, when I-SceI is induced for 48 hr (galactose, Gal) or not induced (raffinose, Raff). (D) Boxplots of the distribution of MSDs at 10 s from Figure 3C for WT and Δrad9 C and S strains. Median values, lower and upper quartiles are shown. Whiskers indicate the full range of measured values, except for outliers represented by small red dots. Parentheses indicate the result of a Wilcoxon rank-sum test between distributions, with the p-value. n.s., non significant, * (p<0.05), ** (p<0.001), *** (p<0.0001).

Figure 3—figure supplement 1—source data 1

qPCR values for I-SceI efficiency.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig3-figsupp1-data1-v1.pdf
Figure 3—figure supplement 1—source data 2

Spot assay for cell survival to I-SceI induction.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig3-figsupp1-data2-v1.zip
Figure 3—figure supplement 1—source data 3

FACS values for cell cycle analysis.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig3-figsupp1-data3-v1.zip
Figure 3—figure supplement 1—source data 4

Mean squared displacement (MSD) values at 10 s.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig3-figsupp1-data4-v1.zip
Figure 4 with 2 supplements
Double-strand break (DSB) induction in the presence of dCen triggers γ-H2A(X) spreading in trans.

(A) H2A phosphorylation spreading measured by chromatin immunoprecipitation (ChIP) around I-SceI cutting site (cs) in strain C or S (in cis) in the absence (gray bars) or in the presence of DSB in the presence of the empty plasmid (white bars) or the dCen plasmid (red bars). ChIP was performed with γ-H2A(X) antibody after 6 hr induction of I-SceI. Uncut control is shown as empty bars. DNA was analyzed by quantitative PCR using ‘in cis’ primers corresponding to sequences at 5, 50, and 100 kb from the right and left sides of I-SceI cs in strains C and S, respectively. Actin was used as the reference gene for each condition. Each bar represents the γ-H2A(X) fold enrichment (γ-H2A(X)-IP/input relative to actin-IP/input) for undamaged and damaged conditions, respectively. The error bars represent the standard deviation of three independent experiments. (B) γ-H2A(X) spreading ‘in trans’ around pericentromeric region of chromosome V. ChIP was performed as above using ‘in trans’ primers corresponding to sequences at 15, 50, and 100 kb from CENV. Note that visualization of the locus on chromosome V (V-Vis) is positioned at 95.7 kb from CENV. (C) Mean squared displacements (MSDs) in strains C and S in H2A-S129A mutated backgrounds. MSDs are calculated as in Figure 2 upon 6 hr of DSB induction with empty plasmid or dCen plasmid (+DSB: n=308 [C strain], n=192 [S strain] and +DSB+dCen: n=205 [C strain], n=198 [S strain], respectively). Controls without DSB are also shown (-DSB: n=352 [C strain], n=88 [S strain]). Five independent experiments were done. Wilcoxon rank-sum test between distributions, with the p-value. n.s., non significant, * (p<0.05), ** (p<0.001). (D) Homologous recombination (HR) kinetics upon induction of I-SceI in the presence of dCen in strains C or S in wild-type (WT) (black) and H2A-S129A (light gray) mutant were measured by FACS as in Figure 1F. Error bars represent the standard deviation of three independent experiments. Wilcoxon rank-sum test between distributions, with the p-value. n.s., non-significant, * (p<0.05), ** (p<0.001).

Figure 4—source data 1

qPCR values after chromatin immunoprecipitation (ChIP) at different indicated genomic positions in cis of the double-strand break (DSB).

https://cdn.elifesciences.org/articles/78015/elife-78015-fig4-data1-v1.zip
Figure 4—source data 2

qPCR values after chromatin immunoprecipitation (ChIP) at different indicated genomic positions in trans of the double-strand break (DSB).

https://cdn.elifesciences.org/articles/78015/elife-78015-fig4-data2-v1.zip
Figure 4—source data 3

Mean squared displacement (MSD) values.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig4-data3-v1.zip
Figure 4—figure supplement 1
Implication of H2AS129 in survival, cell cycle and global dynamics.

(A) I-SceI cleavage efficiency is measured in H2A-S129A, H2A-S129E strains by qPCR using primers flanking the I-SceI cutting site. The error bars represent the standard deviation of two independent experiments. (B) Drop assay (10-fold serial dilutions) showing the sensitivity of wild-type (WT), H2A-S129A and H2A-S129E strains to long exposition to galactose (60 hr), inducing double-strand break (DSB) in strains C and S, with dCen or empty plasmid. As controls, strains C and S not expressing I-SceI are shown. (C) Mean squared displacements (MSDs) in strains C and S in H2A-S129E mutated backgrounds. MSDs are calculated as in Figure 2 upon 6 hr of DSB induction with empty or dCen plasmid (+DSB, n=143 [C strain], n=126 [S strain] and +DSB+dCen, n=200 [C strain], n=176 [S strain], respectively). Controls without DSB are also shown (-DSB: n=925 [C strain], n=90 [S strain]). Five independent experiments were done. (D) Homologous recombination (HR) kinetics upon induction of I-SceI in the presence of dCen in strains C or S on wild-type (WT) (black) and H2A-S129E (gray) background were measured by FACS as in Figure 1F. Error bars represent the standard deviation of three independent experiments.

Figure 4—figure supplement 1—source data 1

qPCR values for I-SceI efficiency.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig4-figsupp1-data1-v1.pdf
Figure 4—figure supplement 1—source data 2

Spot assay for cell survival to I-SceI induction.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig4-figsupp1-data2-v1.zip
Figure 4—figure supplement 1—source data 3

Mean squared displacement (MSD) values.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig4-figsupp1-data3-v1.zip
Figure 4—figure supplement 1—source data 4

Values for repaired red cells.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig4-figsupp1-data4-v1.zip
Figure 4—figure supplement 2
Mean square displacements (MSD) at 10s of V-Vis after a single DSB in the H2AS129 mutants.

(A) Boxplots of the distribution of mean squared displacements (MSDs) at 10 s from Figure 4C and Figure 4—figure supplement 1C , for strains C and S in wild-type (WT) and H2A-S129 mutants without or with a DSB (-DSB, +DSB), with dCen or empty plasmid (+dCen, -dCen). Median values, lower and upper quartiles are shown. Whiskers indicate the full range of measured values, except for outliers represented by small red dots. Parentheses indicate the result of a Wilcoxon rank-sum test between distributions, with the p-value. n.s., non significant, * (p<0.05), ** (p<0.001), *** (p<0.0001).

Figure 4—figure supplement 2—source data 1

Mean squared displacement (MSD) values at 10 s.

https://cdn.elifesciences.org/articles/78015/elife-78015-fig4-figsupp2-data1-v1.zip
Global mobility requires Rad51 only when double-strand break (DSB) and donor sequence are spatially distant.

(A) I-SceI cleavage efficiency is measured in ∆rad51 strains by qPCR using primers flanking the I-SceI cutting site. The error bars represent the standard deviation of three independent experiments. (B) Mean squared displacement (MSD) of the visualization of the locus on chromosome V (V-Vis) locus in strains C (red) or S (blue) mutated for Rad51 (∆rad51) after 6 hr in galactose medium when in the presence of an empty plasmid, I-SceI is not expressed (left, -DSB: n=235 [C strain], n=116 [S strain]), I-SceI is expressed (middle, +DSB: n=416 [C strain], n=368 [S strain]), or I-SceI is expressed in the presence of dCen plasmid (right, +DSB+dCen: n=218 [C strain], n=244 [S strain]). The gray curve corresponds to the control without DSB (-DSB: n=235 [C strain], n=116 [S strain]). Five independent experiments were done. (C) Boxplots of the distribution of MSDs at 10 s from B for strains C and S in wild-type (WT) and ∆rad51 background without or with a DSB (-DSB, +DSB), with dCen or empty plasmids (-dCen, +dCen). Median values, lower and upper quartiles are shown. Whiskers indicate the full range of measured values, except for outliers represented by small red dots. Parentheses indicate the result of a Wilcoxon rank-sum test between distributions, with the p-value. n.s., non significant, * (p<0.05), ** (p<0.001), *** (p<0.0001).

Two types of global mobility are involved in double-strand break (DSB) repair by homologous recombination.

A proximal mobility (left) occurs in the pericentromeric region, a nuclear domain where trans-contacts are enriched. Only H2A phosphorylation is involved in this global mobility, which serves to increase the rate of homologous recombination (HR). By analogy to painting techniques, the proximal mobility could reflect the pouring technique in which oil paint is deposited on water and spreads multidirectionally. It is likely that Mec1 or Tel1 are the factors responsible for this spreading pattern. Distal mobility (right) occurs when DSB is initiated in a region far from the centromeres. The Rad51 nucleofilament is required, as well as HR to promote H2A phosphorylation. The painting analogy here would be that of a paintbrush, with the handle being the Rad51 nucleofilament and the brush being Mec1. The movement of the handle depends on Rad9, and the moving brush allows the deposition of γ-H2A(X). In the absence of Rad51 or Rad9, the brush stays still, decorating only H2A in its immediate environment. The amount of paint deposited will depend on the residence time of the Rad51-ADNsc-Mec1 filament in a given nuclear region. Chromatin decorated by γ-H2A(X) is represented by the orange shadow, at the DSB site and in the pericentromeric region. The red curves represent mobility with thickness symbolizing the amplitude of motion, thin curves for global mobility, and thick curves for local mobility. The lightning bolt represents the DSB.

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  1. Fabiola García Fernández
  2. Etienne Almayrac
  3. Ànnia Carré Simon
  4. Renaud Batrin
  5. Yasmine Khalil
  6. Michel Boissac
  7. Emmanuelle Fabre
(2022)
Global chromatin mobility induced by a DSB is dictated by chromosomal conformation and defines the HR outcome
eLife 11:e78015.
https://doi.org/10.7554/eLife.78015