Using single cell Hi-C to study 3D genome organisation

Cell slice

The spatial organisation of the genome is known to play an important role in regulating RNA transcription to effect cell-type-specific gene expression programs, and to control the differentiation of embryonic stem (ES) cells. Chromatin complexes such as the Nucleosome Remodelling and Deacetylase complex (NuRD) and Chromatin Assembly Factor-1 (CAF-1), are thought to be critical in organising the genome to maintain these gene expression programs.

We have recently developed a single cell Hi-C method, which allows us to image particular proteins and then identify which genomic regions associate with imaged foci in single cells. Using this proximity information we have calculated the first 3D structures of intact mammalian genomes (Stevens et al., 2017; Lando et al., 2018 a,b), and we are now using this approach to understand how complexes such as NuRD regulate chromatin structure and organisation when ES cells differentiate.

For further details see:

  • Stevens TJ, Lando D, Basu S, Atkinson LP, Cao Y, Lee SF, Leeb M, Wohlfahrt KJ, Boucher W, O’Shaughnessy-Kirwan A, Cramard J, Faure AJ, Ralser M, Blanco E, Morey L, Sansó M, Palayret MGS, Lehner B, Di Croce L, Wutz A, Hendrich B, Klenerman D, Laue ED. 3D structures of individual mammalian genomes studied by single-cell Hi-C. Nature 544: 59–64, doi:/10.1038/nature21429 (2017), PMID:28289288
  • Lando D, Basu S, Stevens TJ, Riddell A, Wohlfahrt KJ, Cao Y, Boucher W, Leeb M, Atkinson LP, Lee SF, Hendrich B, Klenerman D, Laue ED. Combining fluorescence imaging with Hi-C to study 3D genome architecture of the same single cell. Nature protocols 13, 1034-1061, doi:10.1038/nprot.2018.017 (2018), PMID:29674753
  • Lando D, Stevens TJ, Basu S & Laue ED. Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols. Nucleus 9, 190-201, doi:10.1080/19491034.2018.1438799 (2018), PMID:29431585

Members of our group currently involved in this project are:

Wayne Boucher, Yang Cao, Dominic Hall, Aleksandra Jartseva, David Lando and Xiaoyan Ma