Histone modifications define distinct nucleosome positions in cell-free DNA
- 1Dana-Farber Cancer Institute
Abstract
Circulating cell-free DNA (cfDNA) fragmentation patterns reflect nucleosome positioning. We asked whether variation in nucleosome positions in cfDNA can reveal chromatin states and associated histone modifications. Using cell-free chromatin immunoprecipitation sequencing (cfChIP-seq) in plasma from patients with prostate cancer, we identified 35,120 modification-associated positions (MAPs), loci where nucleosomes bearing active (H3K4me2) and repressive (H3K9me3) histone marks occupy reproducibly offset positions. These offsets recurred across histone marks, an independent cfChIP-seq cohort, and nuclease-digested chromatin from cell lines. MAPs were enriched in transcribed genes but depleted near transcription start sites and CTCF-binding sites where nucleosome positioning is constrained. Across 2,535 cfDNA sequencing datasets, nucleosome protection at a subset of MAPs correlated with tumor fraction (TF), reflecting differences in histone modification status between cancer-derived and non-malignant chromatin. In targeted sequencing panels, a 50-MAP model using fragments from < 0.001% of the genome distinguished samples with tumor fractions [≥]3% vs 0% (AUCs = 0.91-0.96 across prostate, breast, and lung cancers) and outperformed a state-of-the-art fragmentomics-based tumor fraction predictor. MAP-derived estimates correlated with reference TFs (r = 0.89) and longitudinal changes in TF (r = 0.91). MAP protection at ASCL1 binding sites identified neuroendocrine transformation of prostate cancer from cfDNA. These findings establish histone-modification-associated nucleosome positioning as a mutation-independent readout of tumor fraction and cancer state from routine cfDNA sequencing.
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BibTeX
@misc{ou2026histone,
title = {{Histone modifications define distinct nucleosome positions in cell-free DNA}},
author = {Y. Ou and G. S. Gulati and C. F. Tyndall and M. Pandey and J.-H. Seo and Z. Zhang and Z. Jin and G. G. Lee and R. Nawfal and T. A. Hoggood and S. D. Shahbazi and J. Ludwig and Z. Zhang and E. Ibrahim and G. Nafeh and J. E. Berchuck and A. G. Sowalsky and F. Karzai and M. L. Freedman and D. Y. Takeda and S. C. Baca},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.26.761423},
url = {https://www.biorxiv.org/content/10.64898/2026.10.26.761423v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Histone modifications define distinct nucleosome positions in cell-free DNA
AU - Y. Ou
AU - G. S. Gulati
AU - C. F. Tyndall
AU - M. Pandey
AU - J.-H. Seo
AU - Z. Zhang
AU - Z. Jin
AU - G. G. Lee
AU - R. Nawfal
AU - T. A. Hoggood
AU - S. D. Shahbazi
AU - J. Ludwig
AU - Z. Zhang
AU - E. Ibrahim
AU - G. Nafeh
AU - J. E. Berchuck
AU - A. G. Sowalsky
AU - F. Karzai
AU - M. L. Freedman
AU - D. Y. Takeda
AU - S. C. Baca
PY - 2026
DA - 2026/10/26
PB - bioRxiv
DO - 10.64898/2026.10.26.761423
UR - https://www.biorxiv.org/content/10.64898/2026.10.26.761423v1
AB - Circulating cell-free DNA (cfDNA) fragmentation patterns reflect nucleosome positioning. We asked whether variation in nucleosome positions in cfDNA can reveal chromatin states and associated histone modifications. Using cell-free chromatin immunoprecipitation sequencing (cfChIP-seq) in plasma from patients with prostate cancer, we identified 35,120 modification-associated positions (MAPs), loci where nucleosomes bearing active (H3K4me2) and repressive (H3K9me3) histone marks occupy reproducibly offset positions. These offsets recurred across histone marks, an independent cfChIP-seq cohort, and nuclease-digested chromatin from cell lines. MAPs were enriched in transcribed genes but depleted near transcription start sites and CTCF-binding sites where nucleosome positioning is constrained. Across 2,535 cfDNA sequencing datasets, nucleosome protection at a subset of MAPs correlated with tumor fraction (TF), reflecting differences in histone modification status between cancer-derived and non-malignant chromatin. In targeted sequencing panels, a 50-MAP model using fragments from < 0.001% of the genome distinguished samples with tumor fractions [≥]3% vs 0% (AUCs = 0.91-0.96 across prostate, breast, and lung cancers) and outperformed a state-of-the-art fragmentomics-based tumor fraction predictor. MAP-derived estimates correlated with reference TFs (r = 0.89) and longitudinal changes in TF (r = 0.91). MAP protection at ASCL1 binding sites identified neuroendocrine transformation of prostate cancer from cfDNA. These findings establish histone-modification-associated nucleosome positioning as a mutation-independent readout of tumor fraction and cancer state from routine cfDNA sequencing.
SN - 2692-8205
ER -