Single-molecule regulatory architectures captured by chromatin fiber sequencing

Science. 2020 Jun 26;368(6498):1449-1454. doi: 10.1126/science.aaz1646.


Gene regulation is chiefly determined at the level of individual linear chromatin molecules, yet our current understanding of cis-regulatory architectures derives from fragmented sampling of large numbers of disparate molecules. We developed an approach for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using nonspecific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing of chromatin stencils enabled nucleotide-resolution readout of the primary architecture of multikilobase chromatin fibers (Fiber-seq). Fiber-seq exposed widespread plasticity in the linear organization of individual chromatin fibers and illuminated principles guiding regulatory DNA actuation, the coordinated actuation of neighboring regulatory elements, single-molecule nucleosome positioning, and single-molecule transcription factor occupancy. Our approach and results open new vistas on the primary architecture of gene regulation.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Chromatin / chemistry*
  • Chromatin Assembly and Disassembly*
  • DNA / chemistry
  • DNA / genetics
  • Drosophila melanogaster
  • Gene Expression Regulation*
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • K562 Cells
  • Nucleosomes / chemistry
  • Promoter Regions, Genetic
  • Single Molecule Imaging / methods*
  • Site-Specific DNA-Methyltransferase (Adenine-Specific) / chemistry
  • Transcription Factors / chemistry


  • Chromatin
  • Nucleosomes
  • Transcription Factors
  • DNA
  • Site-Specific DNA-Methyltransferase (Adenine-Specific)