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Science DOI:10.1126/science.aad7701

Single-molecule decoding of combinatorially modified nucleosomes.

Publication TypeJournal Article
Year of Publication2016
AuthorsShema, E, Jones, D, Shoresh, N, Donohue, L, Ram, O, Bernstein, BE
Date Published2016 May 06
KeywordsAnimals, Cell Line, Tumor, Cell Lineage, Cells, Cultured, Chromatin, Epigenesis, Genetic, HEK293 Cells, High-Throughput Nucleotide Sequencing, Histones, Humans, Male, Mice, Molecular Imaging, Nucleosomes, Pluripotent Stem Cells, Proteomics, Sequence Analysis, DNA

Different combinations of histone modifications have been proposed to signal distinct gene regulatory functions, but this area is poorly addressed by existing technologies. We applied high-throughput single-molecule imaging to decode combinatorial modifications on millions of individual nucleosomes from pluripotent stem cells and lineage-committed cells. We identified definitively bivalent nucleosomes with concomitant repressive and activating marks, as well as other combinatorial modification states whose prevalence varies with developmental potency. We showed that genetic and chemical perturbations of chromatin enzymes preferentially affect nucleosomes harboring specific modification states. Last, we combined this proteomic platform with single-molecule DNA sequencing technology to simultaneously determine the modification states and genomic positions of individual nucleosomes. This single-molecule technology has the potential to address fundamental questions in chromatin biology and epigenetic regulation.


Alternate JournalScience
PubMed ID27151869
PubMed Central IDPMC4904710
Grant ListU54 HG006991 / HG / NHGRI NIH HHS / United States
R44HG005279 / HG / NHGRI NIH HHS / United States
/ / Howard Hughes Medical Institute / United States