ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

• Published in: Science (American Association for the Advancement of Science) 2017-07, Vol.357 (6349), p.370-370
• Main Authors: Ou, Horng D., Phan, Sébastien, Deerinck, Thomas J., Thor, Andrea, Ellisman, Mark H., O’Shea, Clodagh C.
• Format: Article
• Language: English
• Subjects: 3,3'-Diaminobenzidine - chemistry; Amino acid sequence; Anthraquinones - chemistry; Assembly; Cell division; Cell fate; Cell Nucleus - ultrastructure; Chromatids; Chromatin; Chromatin - chemistry; Chromatin - ultrastructure; Chromosomes; Compaction; Density; Deoxyribonucleic acid; Distribution patterns; DNA; DNA - chemistry; DNA - ultrastructure; DNA structure; Dyes; Electron microscopy; Epigenetics; Erythrocytes; Fibers; Fluorescence; Fluorescent Dyes - chemistry; Fluorescent indicators; Folding; Gene mapping; Gene sequencing; Genomes; Heredity; Heterochromatin; Histones; Humans; Interphase; Labelling; Measuring instruments; Microscopy; Microscopy, Electron - methods; Mitosis; Nuclei; Nuclei (cytology); Nucleosomes; Nucleosomes - ultrastructure; Nucleotide sequence; Oxidation-Reduction; Packaging; Polymers; Proteins; RESEARCH ARTICLE SUMMARY; Selectivity; Spatial distribution; Spherical coordinates; Staining and Labeling - methods; Tomography; Ultrastructure
• ISSN: 0036-8075; 1095-9203
• DOI: 10.1126/science.aag0025

The chromatin structure of DNA determines genome compaction and activity in the nucleus. On the basis of in vitro structures and electron microscopy (EM) studies, the hierarchical model is that 11-nanometer DNA-nucleosome polymers fold into 30- and subsequently into 120- and 300- to 700-nanometer fibers and mitotic chromosomes. To visualize chromatin in situ, we identified a fluorescent dye that stains DNA with an osmiophilic polymer and selectively enhances its contrast in EM. Using ChromEMT (ChromEM tomography), we reveal the ultrastructure and three-dimensional (3D) organization of individual chromatin polymers, megabase domains, and mitotic chromosomes. We show that chromatin is a disordered 5- to 24-nanometer-diameter curvilinear chain that is packed together at different 3D concentration distributions in interphase and mitosis. Chromatin chains have many different particle arrangements and bend at various lengths to achieve structural compaction and high packing densities.