Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

Cell. 2020 Sep 17;182(6):1641-1659.e26. doi: 10.1016/j.cell.2020.07.032. Epub 2020 Aug 20.


The 3D organization of chromatin regulates many genome functions. Our understanding of 3D genome organization requires tools to directly visualize chromatin conformation in its native context. Here we report an imaging technology for visualizing chromatin organization across multiple scales in single cells with high genomic throughput. First we demonstrate multiplexed imaging of hundreds of genomic loci by sequential hybridization, which allows high-resolution conformation tracing of whole chromosomes. Next we report a multiplexed error-robust fluorescence in situ hybridization (MERFISH)-based method for genome-scale chromatin tracing and demonstrate simultaneous imaging of more than 1,000 genomic loci and nascent transcripts of more than 1,000 genes together with landmark nuclear structures. Using this technology, we characterize chromatin domains, compartments, and trans-chromosomal interactions and their relationship to transcription in single cells. We envision broad application of this high-throughput, multi-scale, and multi-modal imaging technology, which provides an integrated view of chromatin organization in its native structural and functional context.

Keywords: 3D genome organization; MERFISH; chromosome compartments; chromosome conformation; genome-scale imaging; multiplexed FISH; nuclear lamina; nuclear speckles; topologically associated domains; trans-chromosomal interaction.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Cell Line
  • Cell Nucleus / genetics
  • Cell Nucleus / metabolism*
  • Chromatin / genetics
  • Chromatin / metabolism*
  • Chromosomes, Human / genetics
  • Chromosomes, Human / metabolism*
  • DNA / genetics
  • DNA / metabolism
  • Genomics
  • High-Throughput Screening Assays / methods*
  • Humans
  • Image Processing, Computer-Assisted
  • In Situ Hybridization, Fluorescence / methods*
  • Molecular Conformation
  • Multimodal Imaging
  • Nucleolus Organizer Region / genetics
  • Nucleolus Organizer Region / metabolism
  • RNA / genetics
  • RNA / metabolism
  • Single-Cell Analysis / methods*
  • Software


  • Chromatin
  • RNA
  • DNA