Fig. 4: STR expansions in AD are enriched in active promoters and SVA transposable elements.

a Genomic distribution of all (background) STRs tested (top) compared to AD STRs expansions (bottom). b Distribution of distances to nearest TSS for all STRs tested (top) or AD STR expansions (bottom). c Enrichment of AD STR expansions in different chromatin states from the 18-state chromHMM model for adult hippocampus. d Enrichment of AD STR expansions using a permutation-based test. Dotted vertical line shows the number of AD STR expansions observed to overlap “flanking TSS” (chromatin state 2 from chromHMM) in adult hippocampus using a permutation-based test. e Enrichment of AD expanded STRs in peaks from different histone marks based on ChIP-seq in bulk adult hippocampal tissue. f Enrichment of AD STR expansions in different TE classes. g Enrichment of AD expanded STRs in SVA elements using a permutation-based test. h Proportion of STRs at given genomic distances from the nearest SVA. For c,e,f, height of points along the x-axis represents the statistical significance of enrichment, as measured by two-sided Fisher’s exact test. Size of points represents the magnitude of enrichment as represented by the log₂(fold enrichment), and points are ordered by statistical significance for enrichment. For d,g dotted line reflects the observed number of AD STR expansions overlapping the genomic annotation, and histogram represents the number of AD STR expansions overlapping each of 1000 randomly permuted genomic regions. For d,g p-values represent empiric p-values calculated as the number of permutations exceeding observed STR overlap divided by total number of permutations.