title: Single-molecule decoding of combinatorially modified nucleosomes.
abstract: 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.
authors.affiliation: Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Efrat
authors.initials: E
authors.lastname: Shema
authors.affiliation: SeqLL, Woburn, MA 01801, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Jones
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Noam
authors.initials: N
authors.lastname: Shoresh
authors.affiliation: Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Laura
authors.initials: L
authors.lastname: Donohue
authors.affiliation: Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Oren
authors.initials: O
authors.lastname: Ram
authors.affiliation: Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. bernstein.bradley@mgh.harvard.edu.
authors.forename: Bradley E
authors.initials: BE
authors.lastname: Bernstein
mesh_terms: D000818:Animals; D045744:Cell Line, Tumor; D019070:Cell Lineage; D002478:Cells, Cultured; D002843:Chromatin / Q000201:enzymology; D044127:Epigenesis, Genetic; D057809:HEK293 Cells; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006657:Histones / Q000378:metabolism*; D006801:Humans; D008297:Male; D051379:Mice; D057054:Molecular Imaging / Q000379:methods; D009707:Nucleosomes / Q000737:chemistry* / Q000235:genetics*; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D002843:Chromatin; D006657:Histones; D009707:Nucleosomes