title: The visualization of large organized chromatin domains enriched in the H3K9me2 mark within a single chromosome in a single cell.
abstract: Despite considerable efforts, our understanding of the organization of higher order chromatin conformations in single cells and how these relate to chromatin marks remains poor. We have earlier invented the Chromatin In Situ Proximity (ChrISP) technique to determine proximities between chromatin fibers within a single chromosome. Here we used ChrISP to identify chromosome 11-specific hubs that are enriched in the H3K9me2 mark and that project toward the nuclear membrane in finger-like structures. Conversely, chromosome 11-specfic chromatin hubs, visualized by the presence of either H3K9me1 or H3K9me3 marks, are chromosome-wide and largely absent at the nuclear periphery. As the nuclear periphery-specific chromatin hubs were lost in the induced reduction of H3K9me2 levels, they likely represent Large Organization Chromatin in Lysine Methylation (LOCK) domains, previously identified by ChIP-seq analysis. Strikingly, the downregulation of the H3K9me2/3 marks also led to the chromosome-wide compaction of chromosome 11, suggesting a pleiotropic function of these features not recognized before. The ChrISP-mediated visualization of dynamic chromatin states in single cells thus provides an analysis of chromatin structures with a resolution far exceeding that of any other light microscopic technique.
authors.affiliation: a Department of Microbiology; Tumor and Cell Biology ; Stockholm , Sweden.
authors.forename: Xingqi
authors.initials: X
authors.lastname: Chen
authors.forename: Samer
authors.initials: S
authors.lastname: Yammine
authors.forename: Chengxi
authors.initials: C
authors.lastname: Shi
authors.forename: Mariliis
authors.initials: M
authors.lastname: Tark-Dame
authors.forename: Anita
authors.initials: A
authors.lastname: Göndör
authors.forename: Rolf
authors.initials: R
authors.lastname: Ohlsson
mesh_terms: D002843:Chromatin / Q000378:metabolism*; D002880:Chromosomes, Human, Pair 11 / Q000378:metabolism*; D015342:DNA Probes; D005821:Genetic Techniques; D045325:HCT116 Cells; D006657:Histones / Q000378:metabolism; D006801:Humans; D007091:Image Processing, Computer-Assisted; D008239:Lysine / Q000378:metabolism*; D008745:Methylation; D018613:Microscopy, Confocal; D059010:Single-Cell Analysis / Q000379:methods
chemical_list: D002843:Chromatin; D015342:DNA Probes; D006657:Histones; D008239:Lysine
keywords: 3C, chromatin conformation capture; CT11, Chromosome Territory 11; ChIP-seq, chromatin immunoprecipitation sequencing; ChrISP, chromatin in situ proximity; FISH, fluorescence in situ hybridization; LAD, lamin-associated domain; LOCK, Large Organization Chromatin in Lysine Methylation; chromatin; conformation; domains; epigenetics