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3D structures of individual mammalian genomes studied by single-cell Hi-C

2017; Nature Portfolio; Volume: 544; Issue: 7648 Linguagem: Inglês

10.1038/nature21429

1476-4687

Tim J. Stevens, David Lando, Srinjan Basu, Liam P. Atkinson, Yang Cao, Steven F. Lee, Martin Leeb, Kai Wohlfahrt, Wayne Boucher, Aoife O’Shaughnessy-Kirwan, Julie Cramard, André J. Faure, Markus Ralser, Enrique Blanco, Lluís Morey, Miriam Sansó, Matthieu Palayret, Ben Lehner, Luciano Di Croce, Anton Wutz, Brian Hendrich, Dave Klenerman, Ernest D. Laue,

Single-cell and spatial transcriptomics

The folding of genomic DNA from the beads-on-a-string-like structure of nucleosomes into higher-order assemblies is crucially linked to nuclear processes. Here we calculate 3D structures of entire mammalian genomes using data from a new chromosome conformation capture procedure that allows us to first image and then process single cells. The technique enables genome folding to be examined at a scale of less than 100 kb, and chromosome structures to be validated. The structures of individual topological-associated domains and loops vary substantially from cell to cell. By contrast, A and B compartments, lamina-associated domains and active enhancers and promoters are organized in a consistent way on a genome-wide basis in every cell, suggesting that they could drive chromosome and genome folding. By studying genes regulated by pluripotency factor and nucleosome remodelling deacetylase (NuRD), we illustrate how the determination of single-cell genome structure provides a new approach for investigating biological processes. A chromosome conformation capture method in which single cells are first imaged and then processed enables intact genome folding to be studied at a scale of 100 kb, validated, and analysed to generate hypotheses about 3D genomic interactions and organisation. To understand how chromosomes are folded and organized in the nucleus, researchers have taken advantage of microscopy and molecular techniques based on chromosome conformation capture, such as Hi-C. In this paper, Ernest Laue and colleagues describe a novel approach in which they first image and then apply a single-cell Hi-C protocol to individual haploid mouse embryonic stem cells in the G1 phase of the cell cycle. This high-resolution approach allowed the authors to examine how the topological domains and looping of chromosomes vary from cell to cell, at a scale of less than 100 kilobases, and to validate the chromosome structures by imaging.