Data from: RAD51C-XRCC3 complex regulates FANCM-mediated R-loop resolution to safeguard genome integrity
Data files
Jan 08, 2026 version files 236.06 MB
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Alphafold3_Results.zip
83.57 MB
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Fig._1.zip
10.10 MB
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Fig._2.zip
7.48 MB
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Fig._3.zip
216.99 KB
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Fig._4.zip
20.57 MB
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Fig._5.zip
8.36 MB
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Fig._6.zip
7.84 MB
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Fig._7.zip
6.13 MB
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Fig._S1.zip
19.56 MB
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Fig._S10.zip
3.14 MB
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Fig._S2.zip
10.38 MB
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Fig._S3.zip
25.91 MB
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Fig._S4.zip
10.13 MB
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Fig._S5.zip
6.92 MB
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Fig._S6.zip
6.85 MB
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Fig._S8.zip
8.90 MB
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README.md
4.96 KB
Abstract
Fanconi anemia (FA) is characterized by bone marrow failure, congenital abnormalities, and cancer predisposition. Mutations in RAD51 paralogs have been identified in FA-like disorders and cancers. Although the role of RAD51 paralogs is well established in homologous recombination (HR)-mediated DNA repair, little is known about their role during replication stress responses. Here, we report that the RAD51C-XRCC3 (CX3) complex of RAD51 paralogs participates in the FA-pathway of R-loop tolerance mechanism. CX3 complex suppresses R-loops, transcription-replication collisions (TRC), and associated genome instability in physiological and replication stress conditions. Mechanistically, the CX3 complex physically interacts with FANCM and facilitates its recruitment to the R-loop sites to promote its resolution. Notably, cells expressing RAD51C R258H pathological mutant exhibit defective interaction with FANCM and display inefficient R-loop processing. Strikingly, the R-loop resolution function of RAD51C is independent of its ATPase activity, which is required for HR, fork protection, and restart. Collectively, our work identifies a novel role of the CX3 complex in preventing R-loop-induced genome instability by regulating FANCM-mediated R-loop resolution.
Dataset DOI: 10.5061/dryad.mw6m9069c
Description of the data and file structure
All the data, including representative microscopic images, Western blot images, quantification Excel files, and AlphaFold3 structural data, are included in the submitted files.
File Structure:
Organized by Figures and Analysis
Fig. 1
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|- |- 1A data images/ excel file/ blot pdf
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Files and variables
Data processing method:
For S9.6 quantification experiments: Raw nuclear signal intensities for S9.6 were obtained from images of around > 80 cells per sample using ImageJ software. DAPI signal was used as a mask to get nuclear boundary. The mean intensity value for the control sample was calculated. Intensity of all nuclei from all the samples were divided by the mean intensity of the control sample to obtain the "relative S9.6 nuclear intensity" values. The "relative S9.6 nuclear intensity" values for all collected cells were plotted as y-axis of the box-whisker plot against the samples analyzed in the x-axis. For box plots, boxes and whiskers indicate the 25th to the 75th and the 10th to the 90th percentiles, respectively, and median values are indicated. Statistical tests were performed on mean values of three or more biological replicates. P values and the statistical test applied are described in the "analysis" section (sheet) of the Excel file. R1, R2 and R3 sheets in the Excel data files denote the 3 biological repeats.
For other IF foci count experiments: Nuclear foci were counted by applying DAPI signal as mask using the ImageJ software by setting an appropriate "Find Maxima" threshhold value (Threshhold remains same across all samples in a given experiment). As the maxima readout comes in the multiple of 255, the raw foci count numbers were divided by 255 to get the actual foci fount per cell. "Foci count/cell" were plotted as y-axis of the scatter plot against the sample name in the x-axis. Statistical tests were performed on mean values of three or more biological replicates. P values and the statistical test applied are described in the "analysis" section (sheet) of the Excel file. R1, R2, and R3 sheets in the Excel data files denote the 3 biological repeats.
Abbreviations:
The following abbreviations may be used in some of the files for different samples as a short-hand.
| Sample Name | Abbreviations |
|---|---|
| shControl | shCtrl |
| shXRCC3 | shX3 |
| shRAD51C | shC / sh51C / shR51C |
| shXRCC2 | shX2 |
| shFANCD2 | shFD2 |
| shFANCM | shFM |
File: Fig._1.zip
Description: Data corresponding to Main Figure 1 is present in this folder.
File: Fig._2.zip
Description: Data corresponding to Main Figure 2 is present in this folder.
File: Fig._3.zip
Description: Data corresponding to Main Figure 3 is present in this folder.
File: Fig._4.zip
Description: Data corresponding to Main Figure 4 is present in this folder.
File: Fig._5.zip
Description: Data corresponding to Main Figure 5 is present in this folder.
File: Fig._6.zip
Description: Data corresponding to Main Figure 6 is present in this folder.
File: Fig._7.zip
Description: Data corresponding to Main Figure 7 is present in this folder.
File: Fig._S1.zip
Description: Data corresponding to Supplementary Figure 1 is present in this folder.
File: Fig._S2.zip
Description: Data corresponding to Supplementary Figure 2 is present in this folder.
File: Fig._S3.zip
Description: Data corresponding to Supplementary Figure 3 is present in this folder.
File: Fig._S4.zip
Description: Data corresponding to Supplementary Figure 4 is present in this folder.
File: Fig._S5.zip
Description: Data corresponding to Supplementary Figure 5 is present in this folder.
File: Fig._S6.zip
Description: Data corresponding to Supplementary Figure 6 is present in this folder.
File: Fig._S8.zip
Description: Data corresponding to Supplementary Figure 8 is present in this folder.
File: Fig._S10.zip
Description: Data corresponding to Supplementary Figure 10 is present in this folder.
File: Alphafold3_Results.zip
Description: Alphafold modeling data with Figure 5F and 5G, S7 and S9 are present in this folder. The folder contains only selected (model 1) AF3-generated model for WT and R258H RAD51C-XRCC3 complex interaction with FANCM. All the other predicted models of AlphFold3 (for Figs. S7, S9 and S11), including those with the WT CX3 and R258H mutant with FANCM, can be accessed from Model Archive with accession IDs ma-xdl20 and ma-miymb.