Covariate-adjusted AP-1 motif architecture and footprinting track olaparib-adaptive chromatin remodelling

Transcription-factor involvement in drug-adaptive chromatin remodelling is often inferred from motif enrichment in differential ATAC-seq peaks, but such analyses can be distorted by sequence composition, peak length, baseline accessibility and redundant motif models. We reanalysed 105,048 consensus ATAC-seq peaks from an olaparib-adapted Kuramochi ovarian-cancer continuum using HOMER-calibrated AP-1/bZIP models with coordinate-level de-duplication. At T320, 27,154 peaks gained and 30,050 lost accessibility. AP-1 motif-occurrence density remained higher in gained chromatin under complementary adjustments: an all-peak spline-adjusted Poisson model gave a rate ratio of 1.90 (95% CI 1.80-2.01), overlap weighting gave 1.95 (1.82-2.11), and 14,046 covariate-matched pairs gave 1.97 (1.90-2.05). Following 35,325 fixed motif-positive/motif-negative peak pairs across the adapted series showed a positive accessibility trend of 0.0363 contrast units per dose doubling (95% CI 0.0195-0.0531). Raw paired-end ATAC-seq footprinting provided an orthogonal signal: AP-1 motif intervals scored above same-length motif-free controls selected within the same accessible peaks in every sample, and the AP-1-specific footprint score increased by 0.00509 per dose doubling after replicate adjustment (HC3 95% CI 0.00081-0.00937; exact stratified permutation P = 0.00211). In a matched-background genome-wide scan, related AP-1/bZIP models occupied the nine highest ranks. Within gained chromatin, motif-positive peaks showed greater adjusted overlap with pooled public AP-1 summits (OR 3.82, 95% CI 3.52-4.15); after collapsing related files by study, 71 study clusters gave a random-effects OR of 2.68 (2.51-2.87), with substantial heterogeneity and a prediction interval of 1.58-4.54. Multi-model single-cell and independent bulk-RNA analyses indicated context-dependent downstream AP-1 output, whereas the two valid comparable drug-free CRISPR contrasts were not FDR-significant. Exploratory nearest-TSS mapping of AP-1-rich gained peaks identified 899 protein-coding genes; recurring GO, Reactome and KEGG themes and STRING associations were used only to provide qualitative, hypothesis-generating functional context. Together, the data support a robust association between AP-1-compatible chromatin architecture and olaparib adaptation, while not establishing AP-1 occupancy, necessity or sufficiency in the studied cells.