Single-molecule decoding of combinatorially modified nucleosomes

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Science  06 May 2016:
Vol. 352, Issue 6286, pp. 717-721
DOI: 10.1126/science.aad7701

Deciphering the histone code

Regulatory information is stored both in DNA sequences and in the chromatin proteins that package the genome. The covalent modification of histones plays a critical role in signaling whether a gene or genomic region should be active or inactive. Shema et al. used high-throughput single-molecule imaging to reveal the different combinations of modifications on millions of individual nucleosomes. Single-molecule DNA sequencing determined the exact location of these modified nucleosomes in the genome.

Science, this issue p. 717


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.

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