Blood contains cfDNA fragments derived from dying cells 1 . cfDNA has a half-life of ~15 min 2 and, therefore, represents events that occurred close to sampling time. cfDNA analysis is used for assessment of fetus chromosomal aberrations, graft rejection, monitoring tumor dynamics and targeted treatment [3][4][5][6][7] . These applications rely on genetic differences between the host and the tissue of interest. Analysis of CpG methylation in cfDNA is emerging as an alternative independent of genetic alteration 5,[8][9][10][11] . CpG methylation profiles are determined during differentiation and are stable afterwards and, thus, are highly informative about cell identity (for example, liver or lung). However, genetic and methylation-based approaches do not report on recent transcriptional events, as mutations and methylation changes occur over developmental time scales.The basic repeating unit of chromatin is the nucleosome, which is a histone-DNA complex encompassing ~150 base pairs (bp) of DNA 12 . Histone proteins are subject to multiple covalent modifications, which are involved in nearly all aspects of messenger RNA (mRNA) biogenesis [13][14][15][16] . Histone modification patterns reflect recent events related to chromatin regulation and activity of RNA polymerase 13,15 , and different combinations of such modifications mark the location and activity of non-coding regions, enhancers, promoters and gene bodies [17][18][19][20][21][22] . Chromatin immunoprecipitation and sequencing (ChIP-seq) enables genome-wide mapping of histone modifications and provides detailed understanding of the regulatory activity within cells [17][18][19][23][24][25][26][27] .Upon cell death, the genome is fragmented, and chromatin, mostly in the form of nucleosomes, is released into the circulation as cell-free nucleosomes (cf-nucleosomes) 28-30 that retain some histone modifications [31][32][33] . We reasoned that capturing and DNA sequencing of modified nucleosomes from plasma might inform on DNA-related activities, including transcription, within the cells of origin (Fig. 1a). This currently inaccessible epigenetic information extends beyond cfDNA modalities examined to date [4][5][6][7][8][9][10][11][34][35][36][37][38][39][40][41][42][43] .In this study, we performed chromatin immunoprecipitation and sequencing of cell-free nucleosomes directly from human plasma (cfChIP-seq). We show that cfChIP-seq recapitulates the original genomic distribution of modifications associated with transcriptionally active promoters, enhancers and gene bodies, demonstrating that plasma nucleosomes retain the epigenetic information of their

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Blood cell-free DNA (cfDNA) is derived from fragmented chromatin in dying cells. As such, it remains associated with histones that may retain the covalent modifications present in the cell of origin. Until now this rich epigenetic information carried by cell-free nucleosomes has not been explored at the genome level. Here, we perform ChIP-seq of cell free nucleosomes (cfChIP-seq) directly from human blood plasma to sequence DNA fragments from nucleosomes carrying specific chromatin marks. We assay a cohort of healthy subjects and patients and use cfChIP-seq to generate rich sequencing libraries from low volumes of blood. We find that cfChIP-seq of chromatin marks associated with active transcription recapitulates ChIP-seq profiles of the same marks in the tissue of origin, and reflects gene activity in these cells of origin. We demonstrate that cfChIP-seq detects changes in expression programs in patients with 1 heart and liver injury or cancer. cfChIP-seq opens a new window into normal and pathologic tissue dynamics with far-reaching implications for biology and medicine. One Sentence Summary:Chromatin immunoprecipitation and sequencing of histone modifications on blood-circulating nucleosomes (cfChIP-seq) provides detailed information about gene expression programs in different human organs.