Periodic supra-compartment organization of eukaryotic chromosomes

We introduce a coordinate-independent continuous wavelet transform method that, applied to consecutive chromatin accessibility peaks stripped of genomic coordinates, reveals statistically significant periodic organization across all human, mouse, and Drosophila chromosomes at the 5–50 Mbp scale, a supra-compartment tier of genome architecture not previously described. The periodicity corresponds to Hi-C A/B compartments (OR = 10.88), survives IAAFT (p = 0.010) and domain-shuffle (p = 0.005) null models, and is absent in S. cerevisiae and S. pombe, which lack A/B compartmentalization. The periodic wavelength scales with chromosome length across eight eukaryotic species (b = 0.83) but is not explained by block copolymer thermodynamics, reader-writer spreading length, DNA sequence composition, or polymer confinement, seven model tests yield informative nulls. RIF1 knockout causally reduces periodicity coherence (p = 0.017) without altering the wavelength. A-domain crests encode housekeeping genes (OR = 1.60) and are enriched for meiotic recombination hotspots (OR = 1.24, p = 1.5×10⁻⁶); B-domain troughs harbour tissue-specific genes and are crossover-depleted (OR = 0.57). T-cell activation shortens the period (p = 0.006); cardiac differentiation increases it 2.7-fold. The periodicity has a dual origin: its wavelength is geometric; its amplitude is biological.