Chromatin structure shapes circulating cell-free DNA (cfDNA) fragmentation patterns, offering insights into nucleosome organization across the human genome. During apoptosis, nucleosome-bound DNA is protected from nucleases, resulting in cfDNA fragments with a peak at 166 base pairs corresponding to the length of DNA bound by histones. Our study leverages cfDNA to map nucleosome positions, revealing fine-scale details of chromatin architecture.
Using a probabilistic nucleosome protection scoring approach, we mapped cfDNA nucleosome positions across euchromatic and heterochromatic regions. Our analysis uncovered distinct nucleosome repeat lengths (NRLs) associated with two previously described chromatin fiber conformations: T1, characterized by a 182 bp NRL in euchromatin, and T2, with a 187 bp NRL in heterochromatin. This distinction supports the topoisomer model in which chromatin’s functional states are defined by shifts in nucleosome spacing.
Our findings also indicate that nucleosome scoring signals resemble a sine wave, implying that mixed chromatin states in cfDNA should generate wave interference patterns due to the 5 bp NRL difference between euchromatin and heterochromatin. This phenomenon was supported by our analysis of X-chromosome inactivation: in females, the euchromatic regions of the X chromosome, inactive on one homologue, produce a composite nucleosome signal that diminishes the expected NRL differences between euchromatin and heterochromatin. Additionally, we found that nucleosome positioning signals at CTCF binding sites are stronger than those at other transcription factor binding sites and the genome-wide average, suggesting a unique role for CTCF/cohesion loops in organizing nucleosome arrangement and facilitating transitions between chromatin topologies.
We propose a unifying model of chromatin organization in which loop-mediated transitions from T2 to T1 topoisomers regulate chromatin accessibility during interphase and drive compaction during mitosis. This "beads on a looped spring" model highlights chromatin’s adaptive structure and offers a framework to guide future research on how chromatin topology might influence transcriptional accessibility and compaction.