DOI: 10.5061/dryad.zw3r228k1
title: Proteome-wide microarray-based screening of PAR-binding proteins

description: Poly (ADP-ribose) (PAR) plays a crucial role in intracellular signaling
 and scaffolding through covalent modification or non-covalent binding to
 target proteins. The non-covalent PAR binding proteome (PARylome) has not
 been extensively characterized. Here, we performed a PAR-binding screen
 using a human protein microarray that covers most of the human proteome to
 characterize the non-covalent binding PARylome. A total of 356 PAR-binding
 proteins were identified. The PAR-binding PARylome suggests that PAR
 binding regulates a variety of biological processes beyond DNA damage
 signaling and DNA repair. Proteins that may be reprogrammed by PAR binding
 include signaling molecules, transcription factors, nucleic acid-binding
 proteins, calcium-binding proteins, ligases, oxidoreductases, enzymes,
 transferases, hydrolases, and receptors. The global database of
 PAR-binding proteins that we established will be a valuable tool for
 further in-depth analysis of the role of PARylation in a wide range of
 biological contexts.
description: # Proteome-wide microarray-based screening of PAR-binding proteins Dataset
 DOI: [10.5061/dryad.zw3r228k1](https://doi.org/10.5061/dryad.zw3r228k1) ##
 Description of the data and file structure We performed a large-scale
 PAR-binding screen using a human protein microarray to identify proteins
 that interact non-covalently with poly(ADP-ribose) (PAR). This experiment
 characterized the PAR-binding proteome (PARylome) and identified 356
 PAR-binding proteins involved in diverse biological processes beyond DNA
 damage and repair, providing a global resource for studying PAR-mediated
 regulation. Files are labeled by figure and include imaging files, data
 sets in Excel, and graphs in GraphPad. All files included in this
 submission are raw data files generated from experiments performed for
 this manuscript.  ### Files and variables **File: Microarray_Source.zip**
 **Description:** The file "Protein information of the protein
 chip.txt" contains information on all of the proteins spotted in the
 protein microarray. Interpretation keys (explanation) of column headers in
 the table: * Gene ID: ID number annotated by the protein chip maker *
 Chromosomal location: Refers to the specific site on a chromosome * GO -
 Biological Process: Gene ontology by biological process * GO - Cellular
 Component: Gene ontology by cellular component * GO - Molecular Function:
 Gene ontology by molecular function     * RefSeq mRNA Accession: A unique
 identifier assigned by the NCBI Reference Sequence (RefSeq) database to a
 specific, curated messenger RNA (mRNA) sequence, representing a
 non-redundant transcript. * UniGene ID: A unique identifier from the NCBI
 UniGene database that groups together transcripts (including ESTs) that
 appear to come from the same gene (or a single locus). * UniProt
 Accession: A unique, stable identifier for a protein entry in the UniProt
 Knowledgebase (UniProtKB). * UniProt Entry Name: A mnemonic, typically a
 short, descriptive name (often an abbreviation) used to refer to a protein
 entry in the UniProtKB. * UniProt Protein Name: The full, formal name of
 the protein as described in the UniProtKB entry. File RS00283659.gal is
 used for the protein chip reference (Protein coordinate mapping file). Two
 files, "20111123 test chip.tif" and "20111123 test
 chip2.tif", were used for initial background setup and chip quality
 test. Each raw file (.tif), scanned using a GenePix 4000 scanner, can be
 loaded into GenePix Pro software (user
 guide: [https://www.moleculardevices.com/sites/default/files/en/assets/data-sheets/br/genepix-pro-7-software.pdf](https://www.moleculardevices.com/sites/default/files/en/assets/data-sheets/br/genepix-pro-7-software.pdf)) to extract the corresponding images for Anti-mouse Alexa488 and Anti-rabbit Alexa594. From this, the relevant data tables can be generated. **File: 0.Main_Figure_1.zip** **Description:** 0.Main Figure 1.zip including subfolder 1A, 1B, 1C, 1D, 1E, 1F and 1G Figure 1A [Figure 1_subfolder 1A] Subfolder "1A" contains "Figure 1A source image" for illustration. Figure 1Ba [Figure 1_subfolder 1B_subfolder 1Ba] Subfolder "1Ba" contains non-specific negative control background "Control_Poly-A_RS00290793_2013-09-06 (GST).tif" and "Control_Poly-A_RS00290793_2013-09-06", and Poly-A binding images "Poly_A_Set1_RS00283670_2013-04-03", "Poly_A_Set2_RS00283670_2013-04-03", and "Poly_A_Set3_RS00283670_2013-04-03". Figure 1Bb [Figure 1_subfolder 1B_subfolder 1Bb] Subfolder "1Bb" contains "20130416 2000146872_Biotin_PAR_Chip1.jpg" and "20130416 2000146872_Biotin_PAR_Chip2.jpg" for PAR-binding detection using anti-streptavidin antibodies. Figure 1Bc [Figure 1_subfolder 1B_subfolder 1Bc] Subfolder "1Bc" contains "Condition1_PAR_RS00290805_2013-09-18.tif" and "Condition1_PAR-PARG_RS00290805_2013-09-18 (GST).tif" for anti-PAR-based detection for direct PAR-binding confirmation (PARG treatment).  Figure 1C [Figure 1_subfolder 1C] "Table_S1_to_Illustration" contains the 356 PAR-binding proteins, which were statistically filtered by signal intensity. The 15 representative proteins showing the highest affinity out of the 356 PAR-binding proteins are listed in the light orange box.  Abbreviations in the table: IOH Number: An internal identifier used to reference a specific cDNA clone within a database or collection. The acronym IOH stands for Integrated ORF Human, indicating that the clone contains an entire Open Reading Frame (ORF) derived from a human gene. Figure 1D [Figure 1_subfolder 1D] "Table_S2_to_Illustration_2" contains the information of the subcellular localization of the 356 PAR-binding proteins.  Figure 1E [Figure 1_subfolder 1E] "Table_S3_to_Illustration" contains the list of functional classification of the 356 PAR-binding proteins.  Figure 1F [Figure 1_subfolder 1F] "Biogrid_protein_interactions_to_Illustration" contains the list of hub proteins that connects to a high fraction of PAR-binding proteins based on BioGRID analysis (Biological General Repository for Interaction Datasets).  Interpretation keys (explanation) of column headers in the table: * Term: The name or identifier of the biological term or category (e.g., GO term) that the enrichment analysis is based on. * Count: The number of proteins from the input list (352 proteins) that are associated with this specific term. * %: The percentage of the input proteins that are associated with this term (Count / List Total × 100). * Genes: The specific proteins from the list that are annotated to this term. * List total: The total number of proteins in the input (352 proteins) * Pop Hits: The number of proteins in the reference (population) dataset that are annotated with this term. * Pop Total:  The total number of proteins in the entire background (population) dataset used for the analysis. Figure 1G [Figure 1_subfolder 1G] "Table_S4_to_Illustration" contains the information of the classification of the most occurring sequence features found in PAR-binding proteins according to UniProt annotations. Interpretation keys (explanation) of column headers in the table: * Category: The source type within the UniProt database used for feature classification (e.g., UP_SEQ_FEATURE, DOMAIN, COMPBIAS). It describes the general category of the protein feature being analyzed. * Term: The specific UniProt annotation term representing a protein structural or functional element (e.g., DOMAIN:Protein kinase, COMPBIAS:Pro residues, METAL:Calcium 1). This identifies the biological or biochemical feature enriched among the analyzed proteins. **File: 1.Main_Figure_2.zip** **Description:** 1.Main Figure 2.zip including subfolder 2A, 2B, 2C, 2D, 2E, 2F and 2G Figure 2A [Figure 2_subfolder 2A] "Table_S6_to_Illustration" contains the dot plot result, which depicts the distribution of domains and motifs identified from our 17K human protein array and four major screening methods. Abbreviations in the table: * WD40: WD40 repeat domain * BRCT: BRCA1 C-terminal domainz * WWE: A protein–protein interaction module that recognizes ADP-ribose or poly(ADP-ribose) units * FHA: Forkhead-associated domain * OB-fold: Oligonucleotide/oligosaccharide-binding fold (A β-barrel structure that binds single-stranded DNA/RNA or oligosaccharides) * ZNF: Zinc Finger domain * RRM: RNA Recognition Motif * PBM: PAR-Binding Motif * PBZ: PAR-Binding Zinc Finger Figure 2B [Figure 2_subfolder 2B] "Table_S7_to_Illustration" contains a bar graph showing the 12 most common Pfam domain families based on the number of occurrences within the 356 PAR-binding proteins. Figure 2C [Figure 2_subfolder 2C] "Table_S9_to_Illustration" contains the information of two computationally refined versions of previously proposed motifs.  Figure 2D [Figure 2_subfolder 2D] "all_protein_refined_parp_second_domain_result-2.xlsx", "all_protein_update2_original_motif_rev_domain_result-2.xlsx", and "microarray_domain_result.xlsx" contain all the information of amino Acid sequence representations. "Motif1_NewDB_result.xlsx", "Motif2_NewDB_result.xlsx", and "Motif9_NewDB_result.xlsx" contain the 2 most significant motifs, CPxC and CNxC, which are novel PAR-binding domains, using MEME *de novo* amino acid alignment protocol. Amino Acid sequence representation for the most significant motif observed across PAR-binding proteins using the MEGA7 protocol.  Figure 2E [Figure 2_subfolder 2E] Subfolder "2E" contains "Overlapping protein list.txt" for a Venn diagram comparing human proteins containing new CPxC/CNxC motifs and two refined KR motifs, showing that 34 proteins contain all three motifs. Figure 2F [Figure 2_subfolder 2F] Subfolder "Left_panel" contains "Left_Gel01.jpg", "Left_Gel02.jpg", "Left_Gel03.jpg", and "Right_panel" contains "Right_Gel01.jpg", "Right \_Gel02.jpg", "Right \_Gel03.jpg" for native electromobility gel shift assay for the validation of PAR-binding of newly predicted proteins based on the new CPxC/CNxC motifs. Figure 2G [Figure 2_subfolder 2G] "Figure 2G.prism" for intensities of the gel shift assays corresponds to Figure 2F. **File: 2.Main_Figure_3.zip** **Description:** 2.Main Figure 3.zip including subfolder 3A, 3B, 3C, 3D-1(VRK3 data), 3D-2(GSG2 data) and 3E Figure 3 [Figure 3_subfolder 3A] "Table_for_Figure_3A" for a Venn diagram comparing human kinases with new motifs and two refined motifs, showing that 1 kinase contains all three motifs. Figure 3 [Figure 3_subfolder 3B] Subfolder "3B" contains "Gelshift_01.jpg", "Gelshift_02.jpg", and "Representative image Gel_03.jpg" for a native electromobility gel shift assay for the validation of PAR-binding of newly predicted kinases based on the new motifs. Figure 3 [Figure 3_subfolder 3C] "Figure 3C.pzfx" for the intensities of the gel shift assays corresponds to Figure 3B. Figure 3 [Figure 3_subfolder 3D-1] "3D VRK3 and GSG2.prism" for the normalized fluorescence intensity plot corresponds to Figure 3D. Figure 3 [Figure 3_subfolder 3D-2] "3D VRK3 and GSG2.prism" for the normalized fluorescence intensity plot corresponds to Figure 3D. Figure 3 [Figure 3_subfolder 3E] Subfolder "Left panel" "Total H3" contains "Total H3_ch+marke.tif", "Total H3 3rd lane_ch+marke.tif", "Left panel" "AcLys" contains "AcLys+Marker.jpg", "Left panel" "P300" contains "P300+Marker.jpg" for  Ac-Lysine Western blots (Left) for in vitro acetylation assay of p300 on Histone H3 was performed in the presence or absence of pADPr. Subfolder "Middle panel" "Total H3" contains "Total H3K27_ch+marker.tif", "Total H3K27 3rd lane_ch+marker.tif", "Middle panel" "H3K27Ac" contains "K27+Marker.jpg", "Middle panel" "P300" contains "P300+Marker.jpg" for  H3K27Ac Western blots (Middle) for in vitro acetylation assay of p300 on Histone H3 was performed in the presence or absence of pADPr. Subfolder "Right panel" "Total H3" contains "Total H3K36_ch+marker.tif", "Right panel" "H3K36Ac" contains "K36+Marker.jpg", "Right panel" "P300" contains "P300+Marker.jpg" for K36P300+Marker.jpg (Right) for in vitro acetylation assay of p300 on Histone H3 was performed in the presence or absence of pADPr. "Figure 3E" for intensity plots corresponds to Western blots. **File: 3.Main_Figure_4.zip** **Description:** 3.Main Figure 4.zip including subfolder 4A, 4B, 4C, 4D and 4E Figure 4 [Figure 4_subfolder 4A] "Common_XCPXCXX_XCNXCXX (127).txt", "Unique_XCPXCXX (1007).txt", "Unique_XCNXCXX (515).txt" for a Venn diagram comparing human proteins containing the two new PAR-binding motifs, CPxC and CNxC, showing a 127-protein overlap across the two.  Figure 4 [Figure 4_subfolder 4B] "Table_S13_to_Illustration" for a bar chart showing the 3 most significant biological processes, molecular functions, and KEGG pathways for both CPxC and CNxC motifs.  Figure 4 [Figure 4_subfolder 4C] Subfolder "CPXC_Distance" contains "RING-H2_XCPXCXX.txt", "RING-HC_XCPXCXX.txt", "RBQ-1_XCPXCXX.txt", "C4H4_Cnot4_XCPXCXX.txt", "PHD_XCPXCXX.txt", "LIM_XCPXCXX.txt", "All_XCPXCXX.pdf", "RING-HC_XCPXCXX.pdf". "RING-H2_XCPXCXX.pdf", "PHD_XCPXCXX.pdf", "LIM_XCPXCXX.pdf", Subfolder "CNXC_Distance" contains "RING-H2_XCNXCXX.txt", "RING-HC_XCNXCXX.txt", "RBQ-1_XCNXCXX.txt", "C4H4_Cnot4_XCNXCXX.txt", "PHD_XCNXCXX.txt", "LIM_XCNXCXX.txt", "All_XCNXCXX.pdf", "RING-HC_XCNXCXX.pdf". "RING-H2_XCNXCXX.pdf", "PHD_XCNXCXX.pdf", "LIM_XCNXCXX.pdf", and Subfolder "CXXC_Distance" contains "RING-H2.txt", "RING-HC.txt", "RBQ-1.txt", "C4H2C4.txt", "PHD.txt", "LIM.txt", "All.pdf", "RING-HC.pdf". "RING-H2.pdf", "PHD.pdf", "LIM.pdf" for A distance-based graph of motifs CPxC and CNxC with respect to two protein domains, Zinc finger (RING-HC) and E3 Ligase (RING-H2).  Figure 4 [Figure 4_subfolder 4D] "Table_S14_to_Illustration" for a Venn diagram of 614 human protein E3 Ligases containing one or more of PAR-binding motifs: Refined KR motif 1, Refined KR motif 2, and CPxC/CNxC Motif.  Figure 4 [Figure 4_subfolder 4E] "All E3.tif", "All wwp.tif" for a native electromobility gel shift assay for the validation of PAR-binding of E3 ligases, and a graph of corresponding intensities of the gel shift assay.  "Figure 4E E3 Gelshift.prism" for intensities of the gel shift assays corresponds to Figure 4E. **File: 4.Main_Figure_5.zip** **Description:** 4.Main Figure 5.zip including subfolder 5A, 5B, 5C, 5D, 5E, 5F, 5G, 5H, 5I, 5J, 5K and 5L Figure 5 [Figure 5_subfolder 5A] Subfolder "5A" contains "Figure 1A source image" for illustration. Figure 5 [Figure 5_subfolder 5B] "Gel1-1.jpg", "Gel1-2.jpg", "Gel1-3.jpg" for gel shift assay of each of the recombinant wildtype, PBM, and CC mutant of DTX1, DTX2, and RNF4. Figure 5 [Figure 5_subfolder 5C] "Figure 5C.prism" for intensities of the gel shift assays corresponds to Figure 5B. Figure 5 [Figure 5_subfolder 5D] Subfolder "5D" contains "Figure 5D source image" for illustration. Figure 5 [Figure 5_subfolder 5E] "Gel2-1.jpg", "Gel2-2.jpg", "Gel2-3.jpg" for gel shift assay of each of the recombinant wildtype, CC mutant of RNF8, RNF138, and RNF168. Figure 5 [Figure 5_subfolder 5F] "Figure 5F.prism" for intensities of the gel shift assays corresponds to Figure 5E. Figure 5 [Figure 5_subfolder 5G] "Figure 5G.pzfx" for the normalized fluorescence intensity plot corresponds to Figure 5G. Figure 5 [Figure 5_subfolder 5H] "Figure 5H.pzfx" for the normalized fluorescence intensity plot corresponds to Figure 5H. Figure 5 [Figure 5_subfolder 5I] "Figure 5I.pzfx" for normalized fluorescence intensity plot corresponds to Figure 5I. Figure 5 [Figure 5_subfolder 5J] "Figure 5J.pzfx" for normalized fluorescence intensity plot corresponds to Figure 5J. Figure 5 [Figure 5_subfolder 5K] "Figure 5K.pzfx" for normalized fluorescence intensity plot corresponds to Figure 5K. Figure 5 [Figure 5_subfolder 5L] "Figure 5L.pzfx" for normalized fluorescence intensity plot corresponds to Figure 5L. **File: 5.Main_Figure_6-1.zip** **Description:** 5.Main Figure 6-1.zip including subfolder 6Aa, 6Ab, 6Ac, 6Ba and 6Bb Figure 6 [Figure 6_subfolder 6Aa] Subfolder "DTX1 WT" contains "DTX1-WT.jpg", "DTX1-WT1.jpg", "DTX1-WT2.jpg", "DTX1-WT3.jpg", "DTX1-WT4.jpg", Subfolder "DTX1 DM" contains "DTX1-DM.jpg", "DTX1-DM1.jpg", "DTX1-DM2.jpg", "DTX1-DM3.jpg", "DTX1-DM4.jpg" for co-localization between mCherry-FOKI nuclease and each of GFP-fused wildtype- or PBM of DTX1 at DSB site.  Figure 6 [Figure 6_subfolder 6Ab] Subfolder "DTX2 WT" contains "DTX2-WT-dapi.jpg", "DTX2-WT-gfp.jpg", "DTX2-WT-rfp.jpg", "DTX2-WT-merge.jpg", "DTX2-WT-merge1.jpg", Subfolder "DTX2 PBM" contains "DTX2-QD-4.jpg", "DTX2-QD-5.jpg", "DTX2-QD-dapi.jpg", "DTX2-QD-.gfp.jpg", "DTX2-QD-rfp.jpg", "DTX2-QD-merge.jpg", "DTX2-QD-merge1.jpg" for co-localization between mCherry-FOKI nuclease and each of GFP-fused wildtype- or PBM of DTX2 at DSB site. Figure 6 [Figure 6_subfolder 6Ac] Subfolder "RNF4 WT" contains "RNF4-dapi.tif", "RNF4-gfp.tif", "RNF4-rfp.tif", "RNF4-merged.tif", Subfolder "RNF4 PBM" contains "RNF4 QM-dapi.tif", "RNF4 QM-gfp.tif", "RNF4 QM-rfp.tif", "RNF4 QM-merged.tif" for co-localization between mCherry-FOKI nuclease and each of GFP-fused wildtype- or PBM of RNF4 at DSB site. Figure 6 [Figure 6_subfolder 6Ba] Subfolder “DTX1 WT” contains “Image 30.lsm”, “Image 31.lsm”, “Image 32.lsm”, “Image 33.lsm”, “Image 34.lsm”, “Image 35.lsm”, Subfolder “DTX1 DM” contains “Image 64.lsm”, “Image 65.lsm”, “Image 66.lsm”, “Image 67.lsm”, “Image 68.lsm”, “Image 69.lsm”, Subfolder “DTX1 ATMi” contains “Image 80.lsm”, “Image 83.lsm”, “Image 84.lsm”, “Image 86.lsm”, “Image 88.lsm”, “Image 89.lsm”, and Subfolder “DTX1 PARPi” contains “Image 71.lsm”, “Image 72.lsm”, “Image 73.lsm”, “Image 74.lsm”, “Image 75.lsm”, “Image 76.lsm” for cumulative GFP signals at laser strips for (Ba) DTX1 were tested in the presence or absence of PARP inhibitor, PJ34 or ATM inhibitor, KU55933. ”Figure 6Ba.pzfx” for normalized fluorescence intensity plot corresponds to Figure 6Ba. Figure 6 [Figure 6_subfolder 6Bb] Subfolder “DTX2 WT” contains “Image 1.lsm”, “Image 6.lsm”, “Image 7.lsm”, “Image 10.lsm”, “Image 26.lsm”, “Image 28.lsm”, Subfolder “DTX2 DM” contains “Image 15.lsm”, “Image 16.lsm”, “Image 17.lsm”, “Image 19.lsm”, “Image 20.lsm”, “Image 21.lsm”, Subfolder “DTX2 ATMi” contains “Image 3.lsm”, “Image 14.lsm”, “Image 15.lsm”, “Image 17.lsm”, “Image 18.lsm”, “Image 20.lsm”, and Subfolder “DTX2 PARPi” contains “Image 4.lsm”, “Image 8.lsm”, “Image 9.lsm”, “Image 10.lsm”, “Image 11.lsm”, “Image 13.lsm” for cumulative GFP signals at laser strips for (Bb) DTX2 were tested in the presence or absence of PARP inhibitor, PJ34 or ATM inhibitor, KU55933. ”Figure 6Bb.pzfx” for the normalized fluorescence intensity plot corresponds to Figure 6Bb. **File: 6.Main_Figure_6-2.zip** **Description:** 6.Main Figure 6-2.zip including subfolder 6Bc Figure 6 [Figure 6_subfolder 6Bc] Subfolder “RNF4 WT” contains “10sec-1.nd2”, “10sec-2.nd2”, “10sec-3.nd2”, “10sec-4.nd2”, “10sec-5.nd2”, “10sec-6.nd2”, “10sec-7.nd2”, “10sec-8.nd2”, “10sec-8.nd2”, “10sec-10.nd2”, Subfolder “RNF4 QM” contains “QM-1.nd2”, “QM-4.nd2”, “QM-5.nd2”, “QM-10.nd2”, “QM-2_3.nd2”, “QM-6_7.nd2”, “QM-8_9.nd2”, Subfolder “RNF4 ATMi” contains “ATMi.nd2”, “ATMi-2.nd2”, “ATMi-8.nd2”, “ATMi-9.nd2”, “ATMi-10.nd2”, “ATMi-3_4.nd2”, “ATMi-4_5.nd2”, “ATMi-5_6_7.nd2”, and Subfolder “RNF4 PARPi” contains “PAPRi-1.nd2”, “PAPRi-2.nd2”, “PAPRi-5.nd2”, “PAPRi-6.nd2”, “PAPRi-9.nd2”, “PAPRi-3_4.nd2”, “PAPRi-7_8.nd2” for cumulative GFP signals at laser strips for (Bc) RNF4 were tested in the presence or absence of PARP inhibitor, PJ34 or ATM inhibitor, KU55933. ”Figure 6Bc.pzfx” for normalized fluorescence intensity plot corresponds to Figure 6Bc. **File: 7.Main_Figure_7.zip** **Description:** 7.Main Figure 7.zip including subfolder 7Aa, 7Ab, 7Ac, 7Ba, 7Bb, 7Bc, 7Bd, 7Be and 7Bf Figure 7 [Figure 7_subfolder 7Aa] ”DTX1 Colony formation analysis.pzfx” - Clonogenic assay showing that doxycycline-induced expression of DTX1 WT enhances cell survival. Figure 7 [Figure 7_subfolder 7Ab] ”DTX2 Colony formation analysis.pzfx” - Clonogenic assay showing that doxycycline-induced expression of DTX2 WT enhances cell survival. Figure 7 [Figure 7_subfolder 7Ac] ”RNF4 Colony formation analysis.pzfx” - Clonogenic assay showing that doxycycline-induced expression of RNF4 WT enhances cell survival. Figure 7 [Figure 7_subfolder 7Ba] Subfolder “Mock_53BP1” contains “C1-Mock_Blue.jpg”, “C2-Mock_Green.jpg”, “Composite.jpg”, Subfolder “WT_-DOX_53BP1” contains “C1-WT -DOX_10_Blue.jpg”, “C2-WT -DOX_10_Green.jpg”, “Composite.jpg”, Subfolder “WT_+DOX_53BP1” contains “C1-WT +DOX_10_Blue.jpg”, “C2-WT +DOX_10_Green.jpg”, “Composite.jpg”, Subfolder “PBM_-DOX_53BP1” contains “C1-PBM -DOX_04sm_Blue.jpg”, “C2-PBM -DOX_04sm_Green.jpg”, “Composite.jpg”, and Subfolder “PBM_+DOX_53BP1” contains “C1-PBM +DOX_04sm_Blue.jpg”, “C2-PBM +DOX_04sm_Green.jpg”, “Composite.jpg” for 53BP1 foci formation assay. ”Figure 7Ba” for statistical analysis for 53BP1 foci formation assay. Figure 7 [Figure 7_subfolder 7Bb] Subfolder “Mock_BRCA1” contains “C1-Mock_Blue-1.jpg”, “C2-Mock_Red-1.jpg”, “Composite-1.jpg”, Subfolder “WT_-DOX_BRCA1” contains “C1-WT -DOX_Blue.jpg”, “C2-WT -DOX_Red.jpg”, “Composite.jpg”, Subfolder “WT_+DOX_BRCA1” contains “C1_WT_+Dox_Blue.jpg”, “C2-WT +DOX_Red.jpg”, “Composite-1.jpg”, Subfolder “PBM_-DOX_BRCA1” contains “C1-PBM -DOX_Blue.jpg”, “C2-PBM -DOX_Red.jpg”, “Composite.jpg”, and Subfolder “PBM_+DOX_BRCA1” contains “C1-PBM +DOX_Blue.jpg”, “C2-PBM +DOX_Red.jpg”, “Composite.jpg” for BRCA1 foci formation assay. ”Figure 7Bb” for statistical analysis for BRCA1 foci formation assay. Figure 7 [Figure 7_subfolder 7Bc] Subfolder “Mock_53BP1” contains “C1-Mock_12 Blue.jpg”, “C2-Mock_12 Green.jpg”, “Composite12.jpg”, Subfolder “WT_-DOX_53BP1” contains “C1-WT -DOX_04_Blue.jpg”, “C2-WT -DOX_04_Green.jpg”, “Composite.jpg”, Subfolder “WT_+DOX_53BP1” contains “C1-WT +DOX_05_Blue.jpg”, “C2-WT +DOX_05_Green.jpg”, “Composite.jpg”, Subfolder “PBM_-DOX_53BP1” contains “C1-PBM -DOX_11_Blue.jpg”, “C2-PBM -DOX_11_Green.jpg”, “Composite.jpg”, and Subfolder “PBM_+DOX_53BP1” contains “C1-PBM +DOX_07_Blue.jpg”, “C2-PBM +DOX_07_Green.jpg”, “Composite.jpg” for 53BP1 foci formation assay. ”Figure 7Bc” for statistical analysis for 53BP1 foci formation assay. Figure 7 [Figure 7_subfolder 7Bd] Subfolder “Mock_BRCA1” contains “C1-Mock_08 Blue.jpg”, “C2-Mock_08 Red.jpg”, “Composite 08.jpg”, Subfolder “WT_-DOX_BRCA1” contains “C1-WT -DOX_10_Blue.jpg”, “C2-WT -DOX_10_Red.jpg”, “Composite.jpg”, Subfolder “WT_+DOX_BRCA1” contains “C1_WT_+Dox_14_Blue.jpg”, “C2-WT +DOX_14_Red.jpg”, “Composite-1.jpg”, Subfolder “PBM_-DOX_BRCA1” contains “C1-PBM -DOX_04_Blue.jpg”, “C2-PBM -DOX_04_Red.jpg”, “Composite.jpg”, and Subfolder “PBM_+DOX_BRCA1” contains “C1-PBM +DOX_13_Blue.jpg”, “C2-PBM +DOX_13_Red.jpg”, “Composite.jpg” for BRCA1 foci formation assay. "Figure 7Bb” for statistical analysis for BRCA1 foci formation assay. Figure 7 [Figure 7_subfolder 7Be] Subfolder “siNC_V5” contains “sinc-4 dapi.tif”, “sinc-4.tif “, “sinc-4c1.tif”, Subfolder “siRNF4_V5” contains “sirnf4-4 dapi.tif”, “sirnf4-4.tif”, “sirnf4-4c1.tif”, Subfolder “siRNF4_RNF4 WT” contains “rnf4 wt-5 dapi.tif”, “rnf4 wt-5.tif”, “rnf4 wt-5c1.tif”, and Subfolder “siRNF4_RNF4 QM” contains “rnf4 qm-5 dapi.tif”, “rnf4 qm-5.tif”, “rnf4 qm-5c1.tif” for 53BP1 foci formation assay. ”Figure 7Be” for statistical analysis for 53BP1 foci formation assay. Figure 7 [Figure 7_subfolder 7Bf] Subfolder “siNC_V5” contains “sinc-5c1.tif”, “sinc-5c2.tif “, “sinc-5.tif”, Subfolder “siRNF4_V5” contains “sirnf4-1c1.tif”, “sirnf4-1c2.tif”, “sirnf4-1.tif”, Subfolder “siRNF4_RNF4 WT” contains “rnf4 wt-2c1.tif”, “rnf4 wt-2c2.tif”, “rnf4 wt-2.tif”, and Subfolder “siRNF4_RNF4 QM” contains “rnf4 qm-3c1.tif”, “rnf4 qm-3c2.tif”, “rnf4 qm-3.tif” for BRCA1 foci formation assay. ”Figure 7Bf” for statistical analysis for BRCA1 foci formation assay. **File: 8.Supplemental_Figure_1.zip** **Description:** **8.Supplemental Figure 1.zip including subfolder S1A, S1B, S1C, S1D-E, S1F, S1G and S1H, and Reference to 0.Main Figure 1.zip 1B** Supplemental Figure 1 [Supplemental Figure 1 subfolder S1A] ”Silver staining.jpg” for native TBE-PAGE of Biotin-PAR used in this study. Supplemental Figure 1 [Supplemental Figure 1 subfolder S1B] Subfolder “S1B” contains non-specific negative control background “Control_Poly-A_RS00290793_2013-09-06 (GST).tif” and “ Control_Poly-A_RS00290793_2013-09-06”, and Poly-A binding images “ Poly_A_Set1_RS00283670_2013-04-03”, “Poly_A_Set2_RS00283670_2013-04-03” and “Poly_A_Set3_RS00283670_2013-04-03” for Biotin-poly A tail. Supplemental Figure 1 [Supplemental Figure 1 subfolder S1C] Subfolder “S1C” contains “20130416 2000146872_Biotin_PAR_Chip1.jpg” and “20130416 2000146872_Biotin_PAR_Chip2.jpg” for PAR-binding detection using anti-streptavidin antibodies for Biotin-PAR. Supplemental Figure 1 [Supplemental Figure 1 subfolder S1D-E] Subfolder “S1D-E” contains “2000155461_532nm_2014-04-11.tif”, “2000155461_635nm_2014-04-11.tif”, and “2000155461_Dual_2014-04-11.tif” to obtain anti-PAR-based detection. Images obtained using the image in S1E was created by 80x magnifying the marked block in S1D. Supplemental Figure 1 [Supplemental Figure 1 subfolder S1F] Subfolder “S1F” contains “Figure 1F source image” for illustration. Supplemental Figure 1 [Supplemental Figure 1 subfolder S1G] Subfolder “S1G” contains “ Condition1_PAR_RS00290805_2013-09-18.tif” and “Condition1_PAR-PARG_RS00290805_2013-09-18 (GST).tif” for anti-PAR Supplemental Figure 1 [Supplemental Figure 1 subfolder S1H] Subfolder “Upper pannel (IP Flag WB Flag)” contains “1 IP Flag WB Flag .jpg”, “2 IP Flag WB Flag .jpg”, “3 IP Flag WB Flag .jpg”, “4 IP Flag WB Flag .jpg” for Western blot probed with Flag antibody. Subfolder “Bottom Pannel (IP Flag WB HuPAR”19)” contains “1 IP Flag WB 19 .jpg”, “2 IP Flag WB 19 .jpg”, “3 IP Flag WB 19 .jpg”, “4 IP Flag WB 19 .jpg” for PAR overlay Western blot probed with PAR antibody. **File: 9.Supplemental_Figure_2.zip** **Description:** 9.Supplemental Figure 2.zip including subfolder S2A-B, S2C-D, S2E, and S2F Supplemental Figure 2 [Supplemental Figure 2 subfolder S2A-B] Subfolder “S2A-B” contains “Table_S5_to_Illustration.txt” for a Venn diagram comparing PAR-binding protein lists obtained across four different experimental approaches – 17K human protein array, GST-fusion macrodomain screen, PAR antibody-based screen, and boronate-affinity chromatography screen. Supplemental Figure 2 [Supplemental Figure 2 subfolder S2C-D] Subfolder “S2C-D” contains “Table_S7_to_Illustration.txt” for a Venn diagram comparing our experimentally identified protein data lists and computationally predicted PAR-binding protein from previous studies from (C) (Pleschke et al, 2000) and (D) (Gagne, 2008). Supplemental Figure 2 [Supplemental Figure 2 subfolder S2E-F] Subfolder “S2E-F” contains “FigureS2E.tif” for a dot blot using different synthetic peptides of KR-based PAR-binding motifs for S2E, and “Figure S2F SPOT array analysis.xlsx” for PAR-binding intensities corresponding to S2E and S2F. **File: 10.Supplemental_Figure_3.zip** **Description:** 10.Supplemental Figure 3.zip including subfolder S3A, S3B, S3C and S3D Supplemental Figure 3 [Supplemental Figure 3 subfolder S3A] Subfolder “S3A” "MEME-PAR_protein_array_seq_fasta_meme_output” contains “meme.html”, “meme.txt”, “meme.xml”, “logo1.esp to logo10.eps” for sequence representations for 2 significant motifs as novel PAR-binding domains using MEME de novo amino acid alignment protocol. Supplemental Figure 3 [Supplemental Figure 3 subfolder S3B] Subfolder “S3B”glam2_result” contains “glam2.html”, “glam2.txt”, “glam2.xml”, “logo1.esp to logo10.eps”, “logo_ssc1 to logo_ssc10.eps” for sequence representations for 5 most significant motifs observed across PAR-binding proteins using MEGA7 protocol. Supplemental Figure 3 [Supplemental Figure 3 subfolder S3C-D] Subfolder “S3C-D” contains “FigureS3C.tif” for a dot blot using different synthetic peptides of PAR-binding motifs for S3C, and “Figure S3D SPOT array analysis.xlsx” for PAR-binding intensities corresponding to S3C and S3D. **File: 11.Supplemental_Figure_4.zip** **Description:** 11.Supplemental Figure 4.zip including subfolder S4A, S4B, S4C, S4D, S4E, S4F, S4G, S4H, S4I, S4J and S4K Supplemental Figure 4 [Supplemental Figure 4 subfolder S4A] Subfolder “S4A” contains “ Figure S4A source image” for illustration. Supplemental Figure 4 [Supplemental Figure 4 subfolder S4B] Subfolder “S4B” contains “Figure S4B source image” for illustration. Supplemental Figure 4 [Supplemental Figure 4 subfolder S4C] Subfolder “GSG2 WT in WT” contains “00sec100LT.jpg”, “15sec100LT.jpg”, “30sec100LT.jpg”, “60sec100LT.jpg”, “120sec100LT.jpg”, “180sec100LT.jpg”, Subfolder “GSG2 WT in PARP1 KO” contains “00sec10.jpg”, “15sec10.jpg”, “30sec10.jpg”, “60sec10.jpg”, “120sec10.jpg”, “180sec10.jpg”, Subfolder “GSG2 KR1 in WT” contains “00sec05.jpg”, “15sec05.jpg”, “30sec05.jpg”, “60sec05.jpg”, “120sec05.jpg”, “180sec05.jpg”, Subfolder “GSG2 KR2 in WT” contains “00sec09.jpg”, “15sec09.jpg”, “30sec09.jpg”, “60sec09.jpg”, “120sec09.jpg”, “180sec09.jpg”, and Subfolder “GSG2 KR3 in WT” contains “00sec07.jpg”, “15sec07.jpg”, “30sec07.jpg”, “60sec07.jpg”, “120sec07.jpg”, “180sec07.jpg” - Each of GFP-fused wildtype- or PBMs for (C) GSG2 was expressed in either wildtype or PARP1 KO HeLa cells and microirradiated along with the red line as indicated. Supplemental Figure 4 [Supplemental Figure 4 subfolder S4D] Subfolder “VRK3 WT in WT” contains “00sec33.jpg”, “15sec33.jpg”, “30sec33.jpg”, “60sec33.jpg”, “120sec33.jpg”, “180sec33.jpg”, Subfolder “VRK3 WT in PARP1 KO” contains “00sec06.jpg”, “15sec06.jpg”, “30sec06.jpg”, “60sec06.jpg”, “120sec06.jpg”, “180sec06.jpg”, and Subfolder “VRK3 CCDm in WT” contains “00sec78.jpg”, “15sec78.jpg”, “30sec78.jpg”, “60sec78.jpg”, “120sec78.jpg”, “180sec78.jpg” - Each of GFP-fused wildtype- or PBMs for (D) VRK3 was expressed in either wildtype or PARP1 KO HeLa cells and microirradiated along with the red line as indicated. Supplemental Figure 4 [Supplemental Figure 4 subfolder S4E] ”FigS4E.prism” for normalized fluorescence intensity plot corresponds to Figure S4E. Supplemental Figure 4 [Supplemental Figure 4 subfolder S4F] ”FigS4F.prism” for normalized fluorescence intensity plot corresponds to Figure S4F. Supplemental Figure 4 [Supplemental Figure 4 subfolder S4G] Subfolder “S4Ga-S4Gb” contains “EMSA GSG2.jpg” for a gelshift assay of wildtype (GSG2 WT) and PAR binding mutants, (GSG2 Mut”1, GSG2 Mut”2, and GSG2 Mut”3). ”GSG2 Gelshift assay analysis” for an intensity of each free [32P]-PAR, highlighted red dotted box was quantified and plotted Supplemental Figure 4 [Supplemental Figure 4 subfolder S4H] Subfolder “S4Ha-S4Hb” contains “EMSA VRK3_”2.jpg” for a gelshift assay of wildtype (VRK WT) and PAR binding mutants, (VRK CCmut). ”VRK3 Gelshift assay analysis” for an intensity of each free [32P]-PAR, highlighted red dotted box was quantified and plotted. Supplemental Figure 4 [Supplemental Figure 4 subfolder S4I] Subfolder “S4Ia-S4Ib” contains “EMSA P300.jpg” for a gelshift assay of wildtype P300. ”P300 Gelshift analysis.pzfx” for an intensity of each free [32P]-PAR, highlighted red dotted box was quantified and plotted. Supplemental Figure 4 [Supplemental Figure 4 subfolder S4J] Subfolder “S4J” contains “Figure S4J source image” for illustration. Supplemental Figure 4 [Supplemental Figure 4 subfolder S4K] Subfolder “Upper panel” contains “[IP_Flag_WB_PAROL].jpg” for PAR overlay Western blot probed with PAR antibody. Subfolder “Bottom Panel” contains “[IP_Flag_WB_Flag].jpg” for Western blot probed with Flag antibody. - KR motifs in regions between 1,501 and 1,580 amino acids of P300 were mutated and PAR binding of each mutant was tested by PAR overlay assay. **File: 12.Supplemental_Figure_5.zip** **Description:** 12.Supplemental Figure 5.zip including subfolder S5A, S5B, S5C and S5D Supplemental Figure 5 [Supplemental Figure 5 subfolder S5A] Subfolder “S5A” contains “Figure S5A source image” for illustration. Supplemental Figure 5 [Supplemental Figure 5 subfolder S5B] Subfolder “S5B” contains “Figure S5B source image” for illustration. Supplemental Figure 5 [Supplemental Figure 4 subfolder S5C] Subfolder “S5C” contains “Unique_XCPXCXX (1007).txt” for a distance plot of each CPxC motif to various domains: LIM, PHD, RING-H2, and RING-HC. Supplemental Figure 5 [Supplemental Figure 4 subfolder S5D] Subfolder “S5D” contains “Unique_XCNXCXX (515).txt” for a distance plot of each CNxC motif to various domains: LIM, PHD, RING-H2, and RING-HC. **File: 13.Supplemental_Figure_6.zip** **Description:** 13.Supplemental Figure 6.zip including subfolder S6A, S6B and S6C Supplemental Figure 6 [Supplemental Figure 6 subfolder S6A] Subfolder “S6A” contains “Figure S6A source image” for illustration. Supplemental Figure 6 [Supplemental Figure 6 subfolder S6B] Subfolder “S6B”DTX1” contains “DTX1-red.tif”, “DTX1-green.tif”, “DTX1-merge.tif”, Subfolder “S6B”DTX2” contains “DTX2-red.tif”, “DTX2-green.tif”, “DTX2-merge.tif”, Subfolder “S6B”RNF4” contains “RNF4-red.tif”, “RNF4-green.tif”, “RNF4-merge.tif”, Subfolder “S6B”RNF8” contains “RNF8-red.tif”, “RNF8-green.tif”, “ RNF8-merge.tif”, Subfolder “S6B”RNF10” contains “RNF10-red.tif”, “RNF10-green.tif”, “RNF10-merge.tif”, Subfolder “S6B”RNF11” contains “RNF11-red.tif”, “RNF11-green.tif”, “RNF11-merge.tif”, Subfolder “S6B”RNF12” contains “RNF12-red.tif”, “RNF12-green.tif”, “RNF1-merge.tif”, Subfolder “S6B”RNF25” contains “RNF25-red.tif”, “RNF25-green.tif”, “RNF25-merge.tif”, Subfolder “S6B”RNF138” contains “RNF138-red.tif”, “RNF138-green.tif”, “RNF138-merge.tif”, Subfolder “S6B”RNF168” contains “RNF168-red.tif”, “RNF168-green.tif”, “RNF168-merge.tif”, and Subfolder “S6B”HERC3” contains “HERC3-red.tif”, “HERC3-green.tif”, “HERC3-merge.tif” for the screening of DNA damage response (DDR) E3 ligases using the FokI-induced double-strand break (DSB) system. Supplemental Figure 6 [Supplemental Figure 6 subfolder S6C] Subfolder “DTX1 Orthogonal view” contains “z stack.jpg”, “XZ.jpg”, “YX.jpg”, Subfolder “DTX2 Orthogonal view” contains “z stack.jpg”, “XZ.jpg”, “YX.jpg”, Subfolder “RNF4 Orthogonal view” contains “z stack.jpg”, “XZ.jpg”, “YX.jpg”, Subfolder “RNF8 Orthogonal view” contains “z stack.jpg”, “XZ.jpg”, “YX.jpg”, Subfolder “RNF138 Orthogonal view” contains “z stack.jpg”, “XZ.jpg”, “YX.jpg”, and Subfolder “RNF168 Orthogonal view” contains “z stack.jpg”, “XZ.jpg”, “YX.jpg” for validation of PAR-binding E3 ligases identified in S6B by 3D Z-sectioning using confocal microscopy. Subfolder “2.5D View \_DTX1_DTX2_RNF4_RNF8_RNF138_RNF168” contains “DTX1.jpg”, “DTX2.jpg”, “RNF4.jpg”, “RNF8.jpg”, “RNF138.jpg”, “RNF168.jpg” for each right bottom panel for 2.5D view. Subfolder “Intensity plot_DTX1_DTX2_RNF4_RNF8_RNF138_RNF168” contains “Intensity plots two colors.prism” for each intensity plots on each top-right panel. **File: 14.Supplemental_Figure_7.zip** **Description:** 14.Supplemental Figure 7.zip including subfolder S7A, S7B, S7C, S7D, S7E and S7F Supplemental Figure 7 [Supplemental Figure 7 subfolder S7A] Subfolder “DTX1 WT” contains “IVUA DTX1 DTX1.jpg”, “IVUA DTX1 Ub.jpg”, Subfolder “DTX1 Dm” contains “IVUA DTX1 DTX1.jpg”, “IVUA DTX1 Ub.jpg”, and Subfolder “DTX1 CC” contains “IVUA DTX1 DTX1.jpg”, “IVUA DTX1 Ub.jpg”, for in vitro ubiquitination assay using recombinant wildtype, PBMs and CC mutants of DTX1 in the presence or absence of pADPr Supplemental Figure 7 [Supplemental Figure 7 subfolder S7B] Subfolder “DTX2 WT” contains “IVUA DTX2 DTX2.jpg”, “IVUA DTX2 Ub.jpg”, Subfolder “DTX2 Dm” contains “IVUA DTX2 DTX2.jpg”, “IVUA DTX2 Ub.jpg”, and Subfolder “DTX2 CC” contains “IVUA DTX2 DTX2.jpg”, “IVUA DTX2 Ub.jpg”, for in vitro ubiquitination assay using recombinant wildtype, PBMs and CC mutants of DTX2 in the presence or absence of pADPr. Supplemental Figure 7 [Supplemental Figure 7 subfolder S7C] Subfolder “RNF4 WT IVUA” contains “2015_01_27 WT IVUA (a-Ubi).tif”, “2015_01_27 WT IVUA (a-RNF4).tif”, “2014_12_06 WT IVUA (a-Ubi).tif”, “2014_12_06 WT IVUA (a-RNF4).tif”, “2015_01_29 WT IVUA (a-RNF4).tif”, Subfolder “ RNF4 QM IVUA “ contains “2015_03_27 QM IVUA.tif”, “2015_03_29 QM IVUA.tif”, and Subfolder “RNF4 CC” contains “IVUA RNF4 RNF4.jpg”, “IVUA RNF4 Ub.jpg”, for in vitro ubiquitination assay using recombinant wildtype, PBMs and CC mutants of RNF4 in the presence or absence of pADPr. Supplemental Figure 7 [Supplemental Figure 7 subfolder S7D] Subfolder “RNF4 WT” contains “IVUA RNF8 RNF8.jpg”, “IVUA RNG8 Ub.jpg”, and Subfolder “RNF4 CC” contains “IVUA RNF4 RNF4.jpg”, “IVUA RNF4 Ub.jpg”, for in vitro ubiquitination assay using recombinant wildtype, PBMs and CC mutants of RNF4 in the presence or absence of pADPr. Supplemental Figure 7 [Supplemental Figure 7 subfolder S7E] Subfolder “RNF138 WT” contains “IVUA RNF138 RNF138.jpg”, “IVUA RNG138 Ub.jpg”, Subfolder “RNF138 CC1” contains “IVUA RNF138 RNF138.jpg”, “IVUA RNG138 Ub.jpg”, and Subfolder “RNF138 CC2” contains “IVUA RNF138 RNF138.jpg”, “IVUA RNG138 Ub.jpg” for in vitro ubiquitination assay using recombinant wildtype, PBMs and CC mutants of RNF138 in the presence or absence of pADPr. Supplemental Figure 7 [Supplemental Figure 7 subfolder S7F] Subfolder “RNF168 WT” contains “IVUA RNF168 RNF168.jpg”, “IVUA RNG168 Ub.jpg”, and Subfolder “RNF168 CC” contains “IVUA RNF168 RNF168.jpg”, “IVUA RNG168 Ub.jpg” for in vitro ubiquitination assay using recombinant wildtype, PBMs and CC mutants of RNF168 in the presence or absence of pADPr. **File: 15.Supplemental_Figure_8.zip** **Description:** 15.Supplemental Figure 8.zip including subfolder S8Aa, S8Ab, S8Ba, S8Bb and S8C Supplemental Figure 8 [Supplemental Figure 8 subfolder S8Aa] Subfolder “S8Aa” contains “DTX1 gRNA.jpg”, “DTX1 gRNA Actin.jpg” for DTX1 knockdown efficiency. Supplemental Figure 8 [Supplemental Figure 8 subfolder S8Ab] Subfolder “S8Ab” contains “DTX1 Dox onoff.jpg”, “DTX1 Dox onoff actin.jpg” for Dox-inducible rescue of gRNA-resistant DTX1 WT and PBM. Supplemental Figure 8 [Supplemental Figure 8 subfolder S8Ba] Subfolder “S8Ba” contains “DTX2 gRNA.jpg”, “DTX2 gRNA Actin.jpg” for DTX2 knockdown efficiency Supplemental Figure 8 [Supplemental Figure 8 subfolder S8Bb] Subfolder “S8Bb” contains “DTX2 Dox onoff.jpg”, “DTX2 Dox onoff actin.jpg” for Dox-inducible rescue of gRNA-resistant DTX2 WT and PBM. Supplemental Figure 8 [Supplemental Figure 8 subfolder S8C] Subfolder “S8C” contains “RNF4 rescued WB.tif” for RNF4 knockdown efficiency and functional rescue by siRNA-resistant constructs. **File: 16.Supplemental_Figure_9.zip** **Description:** 16.Supplemental Figure 9.zip including subfolder S9A, S9Ba, S9Bb, S9Bc, S9Bd, S9Be and S9Bf Supplemental Figure 9 [Supplemental Figure 9 subfolder S9A] Subfolder “S9A” contains “Figure S9A source image” for illustration. Supplemental Figure 9 [Supplemental Figure 9 subfolder S9Ba] Subfolder “S9Ba” contains “DTX1 HR ASSAYS.pzfx” for an assessment of the effects of DTX1 knockdown on homologous recombination (HR). Supplemental Figure 9 [Supplemental Figure 9 subfolder S9Bb] Subfolder “S9Bb” contains “DTX2 HR ASSAYS.pzfx” for an assessment of the effects of DTX2 knockdown on homologous recombination (HR). Supplemental Figure 9 [Supplemental Figure 9 subfolder S9Bc] Subfolder “S9Bc” contains “RNF4 HR analysis” for an assessment of the effects of RNF4 knockdown on homologous recombination (HR). Supplemental Figure 9 [Supplemental Figure 9 subfolder S9Bd] Subfolder “S9Bd” contains “DTX1 NHEJ ASSAYS.pzfx” for an assessment of the effects of DTX1 knockdown on non-homologous end joining (NHEJ). Supplemental Figure 9 [Supplemental Figure 9 subfolder S9Be] Subfolder “S9Be” contains “DTX2 NHEJ ASSAYS.pzfx” for an assessment of the effects of DTX2 knockdown on non-homologous end joining (NHEJ). Supplemental Figure 9 [Supplemental Figure 9 subfolder S9Bf] Subfolder “S9Bf” contains “RNF4 NHEJ analysis” for an assessment of the effects of RNF4 knockdown on non-homologous end joining (NHEJ)