Supplementary Materials

Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links

Markus Räschle, Godelieve Smeenk, Rebecca K. Hansen, Tikira Temu, Yasuyoshi Oka, Marco Y. Hein, Nagarjuna Nagaraj, David T. Long, Johannes C. Walter, Kay Hofmann, Zuzana Storchova, Jürgen Cox, Simon Bekker-Jensen, Niels Mailand, Matthias Mann

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Supplementary Text
  • Materials and Methods
  • Captions for tables S1 and S2
  • Figs. S1 to S10
  • References
Tables S1 and S2
Table S1. Results from pairwise comparisons and classification. Summary of the results from pairwise comparisons using the SAM algorithm (22). For labelling and experimental conditions see Fig. S1B. Column B-BE report the test results (1: significant, 0: not significant, NA: not detected or not enough valid values). For all tests the significance threshold was an FDR<0.05 at a minimal fold change of 1.5. Column BT-EQ list the fold change and p-value (DIFF: difference of the LOG2 LFQ intensities; PVAL: –LOG10(p-value) of a standard Student's T-test). Volcano plots of each comparison are provided at the end of this supplement. For each time point of experiment EXP03-05 the subset of proteins with significant enrichment on psoralen crosslinked chromatin compared to a mock control was identified. This subset was further evaluated to identify proteins with a specific enrichment on psoralen crosslinked chromatin over the undamaged chromatin. Chromatin binders were defined as proteins with an NP Count > 0 (Column AH, sum of Column G,J,M,P,S,V,Y,AB,AE). Damage-specific chromatin binder (Column AK) were defined as proteins that showed a significant damage-specific enrichment over both controls in at least three conditions (Column AJ, sum of Column I,L,O,R,U,X,AA,AD,AG). Geminin-sensitive chromatin binder (Column F) were defined as proteins which showed at least once a geminin-sensitive enrichment on psoralen crosslinked chromatin (Column B-D). Evaluation of the RPC and pre-RC experiments are shown in Column AL-AO and AQ-AR, respectively (see Fig. S4 for details). For the damage-specific enrichment, a global score and maximum log2 fold change was calculated (reported in Column BF-BG) as described in Materials and Methods.

Table S2. Dynamic recruitment of DNA repair factors to replication forks stalled at psoralen lesions. Relative abundance of the LFQ intensity of each quantified protein (column C-H). A subjective chronological order is provided in (column I). For each replicate the number of identified peptides (column J-AA) and the number of sequenced peptides (column AB-AS) are provided.