Journal: bioRxiv

Article Title: ATM promotes reversed fork processing during DNA interstrand cross-link repair

doi: 10.1101/2025.10.08.680157

Figure Lengend Snippet: a , Model of replication-coupled ICL repair by the FA pathway. b , Schematic describing CRISPR dropout screens using human FANCD2 +/+ or FANCD2 -/- RPE-1 cells. c , Biplot of normZ scores relating viability in psoralen and UVA treated FANCD2 +/+ (y-axis) and FANCD2 -/- (x-axis) RPE-1 cells. d , Immunoblot demonstrating efficiency of PTPA depletion in FANCD2 +/+ and FANCD2 -/- RPE-1 CRISPR knockout cell pools. Cells were transduced with lentivirus carrying non-targeting (NT) and PTPA -targeting sgRNAs. e , Relative RPE-1 cell proliferation after cisplatin treatment was measured using CellTiter-Glo reagent. FANCD2 +/+ and FANCD2 -/- RPE-1 cells were transduced with sgRNAs as in d , and cell proliferation was measured after 5 days. Data represent the mean ± standard deviation from three technical replicates.

Article Snippet: Commercial primary antibody identities and dilutions used for blotting cell samples were as follows: rabbit polyclonal anti-PTPA (human), Cell Signaling Technology #3330, 1:1,000; mouse monoclonal anti-FANCD2 (human), Santa Cruz Biotechnology #sc-20022, 1:1,000; and mouse monoclonal anti-RPA (human), Millipore Sigma #MABE285, 1:1,000.

Techniques: CRISPR, Western Blot, Knock-Out, Transduction, Standard Deviation

Journal: bioRxiv

Article Title: ATM promotes reversed fork processing during DNA interstrand cross-link repair

doi: 10.1101/2025.10.08.680157

Figure Lengend Snippet: a , Lysates from RPE-1 cells used for the chemogenomic screens described in were blotted for FANCD2 and RPA32 (loading control). b , Relative FANCD2 +/+ and FANCD2 -/- RPE-1 cell proliferation after psoralen + UVA treatment was measured using CellTiter-Glo reagent. Cell proliferation was measured after 5 days. Data represent the mean ± standard deviation from two independent experiments.

Article Snippet: Commercial primary antibody identities and dilutions used for blotting cell samples were as follows: rabbit polyclonal anti-PTPA (human), Cell Signaling Technology #3330, 1:1,000; mouse monoclonal anti-FANCD2 (human), Santa Cruz Biotechnology #sc-20022, 1:1,000; and mouse monoclonal anti-RPA (human), Millipore Sigma #MABE285, 1:1,000.

Techniques: Control, Standard Deviation

Journal: bioRxiv

Article Title: ATM promotes reversed fork processing during DNA interstrand cross-link repair

doi: 10.1101/2025.10.08.680157

Figure Lengend Snippet: a , Plasmids were replicated in egg extract supplemented with okadaic acid and the p97 inhibitor NMS-873, as indicated. Replication reactions were blotted for phospho-ATM (S1981) and H3 as in . b , pICL Pt was replicated in mock- or FANCD2-depleted egg extract supplemented with KU-55933, as indicated. Replication reactions were blotted for phospho-ATM (S1981) and H3 as in . c , pICL Pt was replicated in egg extract supplemented with [α- 32 P]dCTP and okadaic acid and the p97 inhibitor NMS-873, as indicated. Replication intermediates were analyzed as in .

Article Snippet: Commercial primary antibody identities and dilutions used for blotting cell samples were as follows: rabbit polyclonal anti-PTPA (human), Cell Signaling Technology #3330, 1:1,000; mouse monoclonal anti-FANCD2 (human), Santa Cruz Biotechnology #sc-20022, 1:1,000; and mouse monoclonal anti-RPA (human), Millipore Sigma #MABE285, 1:1,000.

Techniques:

Journal: bioRxiv

Article Title: ATM promotes reversed fork processing during DNA interstrand cross-link repair

doi: 10.1101/2025.10.08.680157

Figure Lengend Snippet: a , The replication reactions described in were supplemented with [α- 32 P]dCTP, and replication intermediates were resolved on a native agarose gel as in . b , FANCD2 immunodepletion. Egg extracts used in were resolved by SDS-PAGE and blotted for FANCD2. c , The replication reactions described in were supplemented with [α- 32 P]dCTP, and replication intermediates were resolved on a native agarose gel as in . d , pICL Pt was replicated in egg extract supplemented with NMS-873 (to prevent CMG unloading), okadaic acid, and increasing concentrations of linearized pCtrl, as indicated. Replication reactions were blotted for phospho-ATM (S1981) and H3 as in . Addition of linear DNA induces robust ATM activation. e , The pICL Pt replication reactions described in d were additionally supplemented with [α- 32 P]dCTP, and replication intermediates were resolved on a native agarose gel as in . Despite extensive ATM activation, slow figure 8 converged replication fork structures are largely refractory to resection and fork collapse. Red arrowsheads indicate linear plasmids and end-joining products that become labeled due to unscheduled DNA synthesis in extract.

Article Snippet: Commercial primary antibody identities and dilutions used for blotting cell samples were as follows: rabbit polyclonal anti-PTPA (human), Cell Signaling Technology #3330, 1:1,000; mouse monoclonal anti-FANCD2 (human), Santa Cruz Biotechnology #sc-20022, 1:1,000; and mouse monoclonal anti-RPA (human), Millipore Sigma #MABE285, 1:1,000.

Techniques: Agarose Gel Electrophoresis, Immunodepletion, SDS Page, Activation Assay, Labeling, DNA Synthesis

Journal: eLife

Article Title: LIN37-DREAM prevents DNA end resection and homologous recombination at DNA double-strand breaks in quiescent cells

doi: 10.7554/eLife.68466

Figure Lengend Snippet:

Article Snippet: The following antibodies were used for western blot analysis: 53BP1 (Bethyl Laboratories, A300-272A, 1:3000), LIN37 (Santa Cruz Biotechnology, sc-515686, 1:200), BLM (Bethyl Laboratories, A300-572A, 1:2000), BRCA1 for mouse (R and D Systems, gift from Dr. Andre Nussenzweig, NCI, 1:1000) , BRCA1 for human (Millipore Sigma, 07-434, 1:1000), RAD51 (Millipore Sigma, ABE257, 1:2000), BARD1 (Thermo Fisher Scientific, PA5-85707, 1:1000), CtIP (gift from Dr. Richard Baer, [Columbia University, New York], 1:1000), MRE11 (Novus Biologicals, NB100-142, 1:2000), RIF1 (Abcam, ab13422, 1:500), SHLD1/C20orf196 (Thermo Fisher Scientific, PA5-559280, 1:200), GAPDH (Sigma, G8795, 1:10,000), KAP1 (Genetex, GTX102226, 1:2000), FANCD2 (R and D Systems, MAB93691, 1:1000), BRCA2 for human (Proteintech, 19791-1-AP, 1:500), Rb1 (Thermo Fisher Scientific, LF-MA0173, 1:1000), Phospho-Rb (Ser780) (Cell Signaling Technology, 8180T, 1:1000), Phospho-Rb (Ser807/811) (Cell Signaling Technology, 8516T, 1:1000), PCNA (Bethyl Laboratories, A300-276A, 1:3000), CDK4: (Novus Biologicals, NBP1-31308, 1:1000), CDK4 (phosphor Thr 172) (GeneTex, GTX00778, 1:1000), and RPA (Cell Signaling Technology, 2208S, 1:1000).

Techniques: Recombinant, Plasmid Preparation, Genome Wide, CRISPR, Clone Assay, Flow Cytometry, Staining, Sequencing, Software, Microscopy

Journal: eLife

Article Title: LIN37-DREAM prevents DNA end resection and homologous recombination at DNA double-strand breaks in quiescent cells

doi: 10.7554/eLife.68466

Figure Lengend Snippet:

Article Snippet: Antibody , Anti-FANCD2 (Rabbit monoclonal) , R and D Systems , MAB93691 , WB (1:1000).

Techniques: Recombinant, Plasmid Preparation, Genome Wide, CRISPR, Clone Assay, Flow Cytometry, Staining, Sequencing, Software, Microscopy