The limited effects of AAV2 vectors on host chromatin accessibility and nuclear architecture are consistent with a favorable safety profile

Recombinant adeno-associated virus (AAV) vectors are widely used for gene therapeutics, yet their early effects on host chromatin remodeling and nuclear organization remain insufficiently characterized. In contrast, several DNA viruses are known to remodel host chromatin accessibility, for example HSV-1 in mammalian cells and baculoviruses in insect systems. Here we evaluated genome accessibility and nuclear organization of cultured primary human cells at 24 and 48 hours after infection with wildtype AAV2, single-stranded (ss) and self-complementary (sc) recombinant AAV2. Genome-wide ATAC-seq showed no detectable change in host chromatin accessibility at either time point. A DNase I digestion assay at five candidate loci supported this observation. In contrast, immunofluorescence imaging revealed modest decreases in histone H3, H3K27me3, and RNA polymerase II signals, consistent with reduced polymerase engagement under stress-linked pathways. H3K4me3 deviated from this pattern in G1 cells upon scAAV2 infection, where signals increased. Nuclear geometry shifted in parallel with protein signals, with changes in area, perimeter, convexity, and eccentricity. Markers of nuclear condensates also changed, including reduced fibrillarin, SP100, and SRSF2 intensities, altered object shape metrics, and higher counts of promyelocytic leukemia (PML) bodies and nuclear splicing speckles (NSs). Collectively, at the tested doses and times, AAV2-based vectors did not remodel chromatin accessibility at scale and induced only small changes in polymerase associated readouts and nuclear architecture. These data align with a favorable safety profile while highlighting assay limits and suggesting indirect stress related mechanisms.