The Metaphase Chromatin Unit: A Novel Unit of Higher-Order Chromosome Organization in Human Mitotic Cells

Abstract

Background and ObjectivesThe linear relation between human metaphase chromosome length and DNA content has never been rigorously reconciled with modern Hi-C models of mitotic chromatin folding. We tested whether the relation implies a quantitative unit of mitotic chromosome organization. MethodsWe pooled metaphase lengths for 24 human chromosomes from five cytogenetic studies of cultured peripheral lymphocytes and regressed length against base-pair content from GRCh38 and T2T-CHM13 v2.0. Pre-specified analyses comprised ordinary least-squares and power-law fits, arm-level decomposition, and reconciliation with the Gibcus 2018 helical loop-array model. Orthogonal validation used Rao 2014 Hi-C boundary counts and Pope 2014 Repli-Seq. ResultsLength scales linearly with DNA content as L (m) = 0.0329 x Mb + 0.043 (R-squared = 0.998, power-law exponent 0.98 +/- 0.01), with a cross-karyotype compaction density of 33.4 +/- 1.0 nm/Mb. T2T-CHM13 reanalysis identifies satellite over-condensation; the arm-level residual correlates with p-arm fraction (r = 0.65, p = 5.6e-4). We propose an operational Metaphase Chromatin Unit (MCU) as a quantitative scaling unit (not a discrete structural quantum, as quantization tests are negative): 1 MCU = 7.6 Mb DNA = 0.25 m axial length, numerically corresponding to one Gibcus late-metaphase helical turn; the human haploid genome scales to 406 MCUs. The pairwise megabase-shift slope of 32.75 nm/Mb (R-squared = 0.996) and the approximately 6 Mb Abbe optical detection threshold correctly classify 9 of 9 microdeletion syndromes as karyotype-visible versus FISH-required. ConclusionsThe MCU provides a unified quantitative unit for human mitotic chromosome organization, integrating cytogenetic, Hi-C, polymer-biophysical, and clinical scales.