From degraded to deciphered: Applying ATAC-seq to forensic molecular diagnosis under degradation conditions

Standard ATAC-seq protocols were used for library construction and sequencing. Downstream analyses included quality control, differential accessibility analysis, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment, and transcription factor motif analysis. All 12 samples exhibited high-quality sequencing metrics.

Numerous differentially accessible chromatin regions (peaks) were identified between TBI and control groups, demonstrating the sensitivity of ATAC-seq in detecting trauma-associated chromatin alterations. Notably, no significant differences were observed between samples degraded for 0 and 24 hours, indicating the method’s robustness to degradation. Enrichment analyses revealed that differential peaks were significantly associated with biological processes and pathways relevant to TBI pathology, including axon development, synaptic signaling, and neurotrophin signaling pathways.

The SOX transcription factor family emerged as a dominant motif, consistent with known mechanisms of TBI pathophysiology. This study provides compelling evidence that trauma-induced chromatin accessibility changes remain stable even in degraded forensic brain tissues, including those subject to late postmortem intervals. The high sensitivity and specificity of ATAC-seq support its potential application in forensic pathology, offering both a theoretical foundation and empirical validation for its broader use in forensic diagnostics.