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Long-range single-molecule mapping of chromatin accessibility in eukaryotes
Open accessPublished version of a preprint
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 N 6-methyladenosine (m 6 A) 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.
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“single-molecule footprinting methods that use methyltransferases to mark accessible sites11–15 can provide quantitative measurements of these binding states across individual molecules”
From Single-molecule states link transcription factor binding to gene expression (2024) · cites this paper as [14]
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Metadata
- Authors
- Shipony, Z., Marinov, G. K., Swaffer, M. P., Sinnott-Armstrong, N. A., Skotheim, J. M., Kundaje, A., & Greenleaf, W. J.
- Affiliations
- Stanford University (US)
- Chan Zuckerberg Biohub San Francisco (US)
- Corresponding author
- Greenleaf, William J.
- ORCID
- Venue
- Nature Methods
- Published
- 2020-02-10
- Volume
- 17
- Issue
- 3
- Pages
- 319-327
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC7968351
- OpenAlex
- W3004849394
- Cited by
- 160
- References
- 70
- Citations by year
- 2026: 20 · 2025: 23 · 2024: 34 · 2023: 29 · 2022: 18 · 2021: 24 · 2020: 10
- FWCI
- 6.73
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (P50HG007735, 1R01HG008140-01A1, 1UM1HG009442, 1UM1HG009436, 1U01HG009431)
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases (U19AI057266)
- Human Frontier Science Program (RGY006S, LT 000835/2017)
- European Molecular Biology Organization (1119-2016)
- SU | School of Medicine, Stanford University
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- chromatin accessibility, open chromatin, single-molecule long-read sequencing, nanopore sequencing, DNA methylation, N6-methyladenosine, nucleosome positioning, transcription factor binding, distal regulatory elements
- MeSH terms
- Adenosine, Cell Line, Chromatin, Humans, Methylation, Methyltransferases, Nucleosomes, Promoter Regions, Genetic, Protein Binding, Saccharomyces cerevisiae, CpG Islands, DNA Methylation, Chromatin Immunoprecipitation, DNA Fragmentation, High-Throughput Nucleotide Sequencing
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