Concentration-dependent MNase-seq with yeast spike-in normalization resolves nucleosome occupancy and accessibility in human induced pluripotent stem cells (nucMACC)

Micrococcal nuclease sequencing (MNase-seq) maps nucleosome occupancy and positioning genome-wide but is sensitive to digestion conditions and lacks standardized, quantitative normalization. We developed a refined, scalable MNase-seq workflow and applied it to human induced pluripotent stem cells (hiPSCs; FUCCI-reporter line PB010.5) across a five-point MNase digestion titration (0.5, 1, 3, 6, and 10 U), with an in-house Saccharomyces cerevisiae mononucleosomal spike-in (~5% of input DNA) added for cross-sample normalization. Libraries were sequenced on two platforms (Illumina NovaSeq X, 150 bp paired-end; Illumina NextSeq 2000, 50 bp paired-end) and analyzed with the nucMACC pipeline to quantify concentration-dependent shifts between mononucleosomal and subnucleosomal fragments and to resolve the nucleosome-depleted region and +1/-1 nucleosome positioning at transcription start sites. nucMACC accessibility scores stratified nucleosomes into hyper- and hypo-accessible classes corresponding to active and repressive chromatin states.