Fig. 3: Genome-wide occupancy profiles using MNase in archival mouse specimens are the inverse of freshly collected specimens.

A Heatmap of MNase assay significant peak gains and losses (FDR < 0.05, log10Pval < −6) in fresh and archival tissues 2 kb on either side of genome-wide transcription start sites (TSS) pooled across three individuals. B Pooled occupancy values as wiggle traces (DANPOS3 dpeak function) for input (black) and MNase (blue) as well as differential MNase signal over input control (grey) for fresh and archival Mus musculus liver tissue. Occupancy values and signal changes are shown upstream of a gene highly expressed in liver (APOC1, FPKM = 38,660) as measured by RNA-Seq in fresh tissue. Green and orange shading upon the differential signal panel represents significant (FDR < 0.05, log10Pval < −6) peak gains or losses across three individuals detected by DANPOS3. C Venn diagrams demonstrate the relative repeatability of the MNase assay applied to fresh and archival liver tissue among biological replicates in laboratory mice. Numbers/proportions represent genes with significant peak gains for fresh tissue and losses for archival tissue (FDR < 0.05, log10Pval < −6) within 2 kb upstream of the TSS. Lighter colours indicate higher shared gene count. D Differential pooled DANPOS3 occupancy values comparing laboratory strain to wild-caught mice in fresh and archival liver tissue treated with MNase. Signal change is shown for a gene highly upregulated in laboratory versus wild mice (RPP21, log2FC = 9.611) as measured by RNA-Seq analysis of fresh tissue. Green and orange bars represent significant (FDR < 0.05, log10Pval < −6) peak gains or losses detected by DANPOS3. A–D Statistical significance of peak loss or gain was assessed using a two-sided t-test, and the FDR was controlled using the Benjamini–Hochberg procedure to adjust for multiple comparisons. E Genes with pooled occupancy signal changes (Fresh = gains; Archival = losses) show highest enrichment (fold change over a set of all mouse protein-coding genes) for genes expressed in the liver in both fresh and archival mouse tissues. For each panel, shared gene lists were assembled from a pool of three laboratory and three wild mice and enrichment within Mouse ENCODE datasets was calculated with TissueEnrich. Statistical significance of enrichment was assessed using a hypergeometric test, and the FDR was controlled using the Benjamini–Hochberg procedure.* Significant (Benjamini–Hochberg adjusted p-value < 0.001) enrichment above background. Source Data are provided as a Source Data file.