SUPPLEMENTARY FIGURE LEGENDS
Figure S1. The expression of the MBD chimera rescues checkpoint-adaptation defect in slx4∆ cells.
Graph shows the percentage of adapted cells for each mutant 24 hours after plating on galactose containing
medium to induce one irreparable HO-cut. Values are the mean of three independent experiments ±
standard deviation.
Figure S2. Rad9 binding on chromosome III following induction of a DSB.
Rad9 was subjected to ChIP-seq analysis at the indicated times after induction of HO endonuclease, in wild
type and slx4∆ strains. The enrichment scores (from the experiment in Figure 2A) are plotted across the
entire length of chromosome III. The HO cut site is at the MAT locus (~0.2 Mb).
We think that the fast decrease of Rad9 binding around ~0.05Mb, both in wild type and slx4∆ cells, is likely a
consequence of a chromatin change and gene expression following galactose addition. Interestingly, the
GLK1 gene, whose expression is important for carbon source metabolism, is located in that region. At the
moment, we have no evidence that Rad9 binding decrease at ~0.05Mb position can be correlated to the
DSB formation at MAT locus, which is far away.
Table S1. Yeast strains used in the study.
Table S2. DNA oligonucleotides used in the study.
Figure S1
slx4∆ MBD
slx4∆
wild type
0
20
40
60
% of adapted cells
80
100
Figure S2
2
Rad9-HA ChIP
0 hr
1
Enrichment (log2 IP/input)
0
2
2 hr
1
0
2
4 hr
1
0
2
6 hr
1
0
0.00
0.05
0.10
0.15
0.20
0.25
0.30
Chromosome III Location (MB)
2
Rad9-HA ChIP in slx4∆
0 hr
1
Enrichment (log2 IP/input)
0
2
2 hr
1
0
2
4 hr
1
0
2
6 hr
1
0
0.00
0.05
0.10
0.15
0.20
Chromosome III Location (MB)
0.25
0.30
Table S1. List of yeast strains described in this work.
Strain
name
Y1264
Parental strain
Genotype
Source
W303
MATa ade2- 1 ura3-1 his3-11,15 trp1-1
leu2-3,112 can1-100
Lab stock
Y1600
JKM179
Lee et al., 1998
Y1126
JKM139
Y602
Y603
Y1600
tGI354
Y642
Y1912
Y2170
Y2192
Y2194
Y2258
Y2259
Y2448
Y2451
Y2453
Y2446
Y2456
Y1600
Y1600
Y1912 X Y95
Y1600
Y602
Y1912
Y1912
Y2452 X Y2416
Y1264
W303
Y2452 X Y2416
Y603 X Y2259
Y2462
Y2517
Y2561
Y1943 X Y602
Y2452 X Y2478
Y2258
Y2607
Y2452 X Y2565
Y2609
Y2452 X Y2565
Y2617
Y2619
Y1600
Y2192
Y2648
Y2258
Y2719
Y2403 X Y2618
Y2726
Y1912
Y2727
Y2729
Y2828
Y1600
Y1912
Y2728 X Y2675
Y2832
Y2950
Y3060
Y2729 X Y2675
Y603
Y603
MATa ho hml::ADE1 hmr::ADE1 ade1100 leu2-3, 112 lys5, trp1::hisG ura3-52
lys5::ade3::GAL10::HO
MATalpha ho hml::ADE1 hmr::ADE1
ade1-100 leu2-3, 112 lys5, trp1::hisG
ura3-52 lys5::ade3::GAL10::HO
MATa rad9::KANMX6
ho hml∷ADE1 MATa-inc hmr∷ADE1
ade1 leu2-3,112 lys5 trp1∷hisG ura3-52
ade3∷GAL∷HO (arg5,6∷MATa∷HPH)
MATa sae2::KANMX6
MATa slx4::HPH
MATa slx4::HPH sae2::KANMX6
MATa rtt107::HPH
MATa rad9::KANMX6 rtt107::HPH
MATa SLX4-FLAG::KANMX6
MATa slx4-S486A-FLAG::KANMX6
MATa cdc13-1 rad9::HIS3 slx4::HPH
MATa cdc13-1 rad9::HIS3
MATa cdc13-1
MATa cdc13-1 slx4::HPH
MATa slx4-S486A-FLAG::KANMX6
rad9::KANMX6
MATa rad9::KANMX6 slx4::HPH
MATa cdc13-1 rtt107::HPH
MATa SLX4-FLAG::KANMX6
rtt107::HPH
MATa cdc13-1 slx4-S486AFLAG::KANMX6 rad9::HIS3
MATa cdc13-1 slx4-S486AFLAG::KANMX6
MATa RAD9::3XHA::KANMX6
MATa rtt107::HPH
RAD9::3XHA::KANMX6
MATa SLX4-FLAG::KANMX6
ddc1::TRP1
MATa slx4-S486A-FLAG::KANMX6
RAD9::3XHA::KANMX6
MATa slx4::HPH
RAD9::3XHA::KANMX6
MATa ddc1-T602A::KANMX6
MATa slx4::HPH ddc1-T602A::KANMX6
MATa ddc1-T602A::KANMX6
RAD9::3XHA::KANMX6
MATa slx4::HPH ddc1-T602A::KANMX6
rad9::URA3
slx4::NAT
Lee et al., 1998
Ferrari et al., 2015
Ira et al., 2003
Ferrari et al., 2015
This study
This study
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Lazzaro et al., 2008
Lazzaro et al., 2008
This study
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Ferrari et al., 2015
This study
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Y3069
Y3075
Y3083
Y3085
Y3100
Y3115
Y3117
Y3120
Y3138
Y3160
Y603
Y603
Y603
Y603
Y1600
Y603
Y603
Y603
Y603
Y603
rtt107::NAT
slx4::NAT sae2::URA3
slx4-S486A::KAN
sae2::KAN
slx1::HPH rad1::HPH mus81::HPH
sae2::KAN rtt107::NAT
slx4-S486A::KAN sae2::URA3
sae2::KAN rad9::URA3 rtt107::NAT
sae2::URA3 slx4-S486A::KAN rad9::NAT
sae2::URA3 slx4::NAT rad9::KAN
This study
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Table S2. List of the oligonucleotides used for ChIP and DSB resection analyses.
Name QMAT2.F QMAT2.R QMAT3.1.F QMAT3.1.R QPRE1.F QPRE1.R QARO1.F QARO1.R Sequence (5’-­‐3’) ATTGCGACAAGGCTTCACCC CCACATCACAGGTTTATTGGTTCC GGTTCAACAACTGCCACCTTTG GGTGATGGAGATGGAGTAGGAACG CCCACAAGTCCTCTGATTTACATTCG ATTCGATTGACAGGTGCTCCCTTTTC GAGTCGTTACAAGGTGATGCCAG AATAGCGGCAACAACACATGC Distance from DSB 4,8 kb (ChrIII) 4,8 kb (ChrIII) 10 kb (ChrIII) 10 kb (ChrIII) Chr V Chr V Chr IV Chr IV Source Kim et al. 2007 Kim et al. 2007 This study This study Shim et al. 2005 Shim et al. 2005 This study This study