Long-range single-molecule mapping of chromatin accessibility in eukaryotes

Nat Methods. 2020 Mar;17(3):319-327. doi: 10.1038/s41592-019-0730-2. Epub 2020 Feb 10.

Abstract

Mapping open chromatin regions has emerged as a widely used tool for identifying active regulatory elements in eukaryotes. However, existing approaches, limited by reliance on DNA fragmentation and short-read sequencing, cannot provide information about large-scale chromatin states or reveal coordination between the states of distal regulatory elements. We have developed a method for profiling the accessibility of individual chromatin fibers, a single-molecule long-read accessible chromatin mapping sequencing assay (SMAC-seq), enabling the simultaneous, high-resolution, single-molecule assessment of chromatin states at multikilobase length scales. Our strategy is based on combining the preferential methylation of open chromatin regions by DNA methyltransferases with low sequence specificity, in this case EcoGII, an N6-methyladenosine (m6A) methyltransferase, and the ability of nanopore sequencing to directly read DNA modifications. We demonstrate that aggregate SMAC-seq signals match bulk-level accessibility measurements, observe single-molecule nucleosome and transcription factor protection footprints, and quantify the correlation between chromatin states of distal genomic elements.

Publication types

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

MeSH terms

  • Adenosine / analogs & derivatives
  • Adenosine / chemistry
  • Cell Line
  • Chromatin / chemistry*
  • Chromatin Immunoprecipitation
  • CpG Islands
  • DNA Fragmentation*
  • DNA Methylation
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Methylation
  • Methyltransferases / genetics
  • Nucleosomes / chemistry
  • Promoter Regions, Genetic
  • Protein Binding
  • Saccharomyces cerevisiae / chemistry*

Substances

  • Chromatin
  • Nucleosomes
  • N-methyladenosine
  • Methyltransferases
  • Adenosine