Journal: bioRxiv

Article Title: High resolution interaction surface mapping by PRISMA reveals novel ARID1A interactions

doi: 10.64898/2026.03.15.711656

Figure Lengend Snippet: A, Curated ARID1A physical interaction map. Coloured boxes in ARID1A diagram represent significant domains, regions of motifs. The top graph represents intrinsic disorder regions (IDR). Intrinsic disorder scores were calculated with IUPred2A ( https://iupred2a.elte.hu/ ). The blue line represents the IUPred2 prediction (disordered protein regions) and the orange line represents the ANCHOR2 prediction (disordered binding regions). Scores above 0.5 represent intrinsic disorder. B, PRISMA experimental workflow. Nuclear lysates from RPE1 cells were incubated with an ARID1A tiled peptide array. After membrane washes the individual peptide spots containing binding proteins were processed and analysed by mass spectrometry. C, PRISMA data analysis workflow . D, Clustered heat-map of PRISMA binding profiles aligned with the ARID1A protein diagram and IUPred2A predictions, representing data from a single biological replicate with technical replicate MS measurements for 50% of peptide spots. Only proteins that were identified by at least two peptides were used, and the two replicate datasets were integrated by calculating the average LFQ intensity (hereafter intensity) for each protein in each spot where two measurements were available or using the single available value. The signal intensity for each protein across the 228 bait peptides was then normalised between 0 and 1. See also Tables S1 and S2 and Figures S1 and S2.

Article Snippet: The PRISMA membrane was wetted for 15 mins in PRISMA detergent-free wash buffer (50 mM HEPES pH 8.0, 150 mM NaCl, 1 mM EDTA, 10% glycerol), followed by blocking with yeast tRNA at 1 mg/ml (Life Technologies) in the same buffer.

Techniques: Binding Assay, Incubation, Peptide Microarray, Membrane, Mass Spectrometry

Journal: bioRxiv

Article Title: High resolution interaction surface mapping by PRISMA reveals novel ARID1A interactions

doi: 10.64898/2026.03.15.711656

Figure Lengend Snippet: A, ARID1A PRISMA profiles of BAF subunits . B, Detailed comparison of PRISMA data on BAF subunits to amino acid contacts in cryoEM model structure 6LTH and XL-MS data of the SWI/SNF complex . No contacts between ARID1A and ACTL6A were observed in cryoEM structure 6LTH. Contacts by different paralog subunits are represented where available.

Article Snippet: The PRISMA membrane was wetted for 15 mins in PRISMA detergent-free wash buffer (50 mM HEPES pH 8.0, 150 mM NaCl, 1 mM EDTA, 10% glycerol), followed by blocking with yeast tRNA at 1 mg/ml (Life Technologies) in the same buffer.

Techniques: Comparison, Structural Proteomics

Journal: bioRxiv

Article Title: High resolution interaction surface mapping by PRISMA reveals novel ARID1A interactions

doi: 10.64898/2026.03.15.711656

Figure Lengend Snippet: A, PRISMA profiles of ARID1A mapped interacting partners . B, PRISMA detects YAP1 binding to a PPXY SLiM in ARID1A. ELMdb represents Eukaryotic Linear Motifs database annotation of PPxY motifs (LIG_WW_1) on ARID1A. Intensity scale as in A.

Article Snippet: The PRISMA membrane was wetted for 15 mins in PRISMA detergent-free wash buffer (50 mM HEPES pH 8.0, 150 mM NaCl, 1 mM EDTA, 10% glycerol), followed by blocking with yeast tRNA at 1 mg/ml (Life Technologies) in the same buffer.

Techniques: Binding Assay

Journal: bioRxiv

Article Title: High resolution interaction surface mapping by PRISMA reveals novel ARID1A interactions

doi: 10.64898/2026.03.15.711656

Figure Lengend Snippet: A, Alignment of the SIN3A PRISMA binding profile to ARID1A tiled peptide array and the Sin3 SLiM ELM prediction on ARID1A . B, Bar graph representing levels of SIN3A on chromatin in ARID1A KO and parental RPE1 cells (n=3, mean ± SD, * p< 0.05, *** p< 0.00005). C, Co-immunoprecipitation of endogenous SIN3 complex (circled) by ARID1A C-terminal fragment GFP pulldown. D, Schematic of the in vitro binding experiment between recombinant ARID1A-V5 and SIN3A fragment (449-1086) containing the PAH3 domain tagged with StrepII tag. E, Co-immunoprecipitation of recombinant ARID1A-V5 and SIN3A_PAH3-StrepII. ARID1A-V5 was immunoprecipitated from insect cell lysates. IgG was used as a negative control. Beads were then incubated with cell lysate from insect cells expressing SIN3A_PAH3-StrepII. Co-immunoprecipitation was assessed with anti-V5 and anti-StrepII antibodies to detect ARID1A and SIN3A_PAH3 respectively. KDM5A-StrepII was used as a positive control. Lanes labelled with X are irrelevant for this work.

Article Snippet: The PRISMA membrane was wetted for 15 mins in PRISMA detergent-free wash buffer (50 mM HEPES pH 8.0, 150 mM NaCl, 1 mM EDTA, 10% glycerol), followed by blocking with yeast tRNA at 1 mg/ml (Life Technologies) in the same buffer.

Techniques: Binding Assay, Peptide Microarray, Immunoprecipitation, In Vitro, Recombinant, Negative Control, Incubation, Expressing, Positive Control

Journal: bioRxiv

Article Title: High resolution interaction surface mapping by PRISMA reveals novel ARID1A interactions

doi: 10.64898/2026.03.15.711656

Figure Lengend Snippet: A, TOX4 PRISMA binding profile to ARID1A tiled peptide array. Predicted PLK1 consensus sites in TOX4-binding ARID1A peptides are shown . B, AlphaFold structural models of TOX4 with the two ARID1A peptides where TOX4 binding signal was detected. C, Co-immunoprecipitation of TOX4 and ARID1A. TOX4 was immunoprecipitated from RPE1 and HEK293T cells. IgG was used as a negative control. TOX4 immunoprecipitates were probed for the presence of ARID1A and ubiquitin. Short and long exposures are shown for ARID1A detection.

Article Snippet: The PRISMA membrane was wetted for 15 mins in PRISMA detergent-free wash buffer (50 mM HEPES pH 8.0, 150 mM NaCl, 1 mM EDTA, 10% glycerol), followed by blocking with yeast tRNA at 1 mg/ml (Life Technologies) in the same buffer.

Techniques: Binding Assay, Peptide Microarray, Immunoprecipitation, Negative Control, Ubiquitin Proteomics

Journal: bioRxiv

Article Title: High resolution interaction surface mapping by PRISMA reveals novel ARID1A interactions

doi: 10.64898/2026.03.15.711656

Figure Lengend Snippet: A, CDK2 and cyclin A2 PRISMA binding profiles with zoomed in sections of CDK2/CCNA2 binding overlap and CDK2 phosphorylation site on ARID1A. B, Validation of CDK2/CCNA2 binding to a subset of ARID1A peptides by far-western blotting using a recombinant mix of CDK2/CCNA2. WT, wild type peptide sequence; SCR, scrambled sequence control. C, Validation of CCNA2 direct binding to a subset of ARID1A peptides by far-western blotting using recombinant CCNA2. Peptides as in B. D, Heatmap showing levels of phosphorylated S363 (normalised to ARID1A abundance) along the cell cycle. See also Table S4.

Article Snippet: The PRISMA membrane was wetted for 15 mins in PRISMA detergent-free wash buffer (50 mM HEPES pH 8.0, 150 mM NaCl, 1 mM EDTA, 10% glycerol), followed by blocking with yeast tRNA at 1 mg/ml (Life Technologies) in the same buffer.

Techniques: Binding Assay, Phospho-proteomics, Biomarker Discovery, Far Western Blot, Recombinant, Sequencing, Control