ArticleeLife2020
Massively multiplex single-molecule oligonucleosome footprinting.
Article in eLife, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
84 citing papers in PubMed.
- Decoding chromosome organization using proximity labeling and long-read sequencing.Journal of genetics and genomics = Yi chuan xue bao · 2026Article
- A practical guide to studying genome function using single-molecule genomics.Nature reviews. Molecular cell biology · 2026Review
- Cumulative transcription factor binding and p300-mediated histone acetylation drive enhancer activation frequency.Nature genetics · 2026Article
- Segmentally Duplicated Regulatory Elements Undergo Human-Specific Rewiring.Molecular biology and evolution · 2026Article
- Mapping Protein Occupancy on DNA with an Unnatural Cytosine Modification.ACS chemical biology · 2026Article
- Single-molecule nucleosome spacing coordinates chromatin fiber interactions.bioRxiv : the preprint server for biology · 2026Article
- Article
- Nucleosome remodeling by a CHD enzyme promotes H3K9 methylation establishment and spreading via remodeler-writer feedback.bioRxiv : the preprint server for biology · 2026Article
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- SMTrackR: an R/Bioconductor package for mapping protein binding at individual DNA molecules.Bioinformatics advances · 2026Article
- Direct measurement of sub-kilobase chromatin structure reveals that linker histone H1 broadly compacts chromatin, with differential impact amongst epigenetic states.bioRxiv : the preprint server for biology · 2025Article
- Mapping single-cell diploid chromatin fiber architectures using DAF-seq.Nature biotechnology · 2025Article
- ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes.Science (New York, N.Y.) · 2025Article
- Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase.Nature methods · 2025Article
- The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers.bioRxiv : the preprint server for biology · 2025Article
- HMGB1 deforms nucleosomal DNA to generate a dynamic chromatin environment counteracting the effects of linker histone.Science advances · 2025Article
- SMAdd-seq: probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing.Nucleic acids research · 2025Article
- Nucleosome spacing can fine-tune higher-order chromatin assembly.Nature communications · 2025Article
- A haplotype-resolved view of human gene regulation.bioRxiv : the preprint server for biology · 2025Article
- Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming.Genome biology · 2025Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
Our understanding of the beads-on-a-string arrangement of nucleosomes has been built largely on high-resolution sequence-agnostic imaging methods and sequence-resolved bulk biochemical techniques. To bridge the divide between these approaches, we present the single-molecule adenine methylated oligonucleosome sequencing assay (SAMOSA). SAMOSA is a high-throughput single-molecule sequencing method that combines adenine methyltransferase footprinting and single-molecule real-time DNA sequencing to natively and nondestructively measure nucleosome positions on individual chromatin fibres. SAMOSA data allows unbiased classification of single-molecular 'states' of nucleosome occupancy on individual chromatin fibres. We leverage this to estimate nucleosome regularity and spacing on single chromatin fibres genome-wide, at predicted transcription factor binding motifs, and across human epigenomic domains. Our analyses suggest that chromatin is comprised of both regular and irregular single-molecular oligonucleosome patterns that differ subtly in their relative abundance across epigenomic domains. This irregularity is particularly striking in constitutive heterochromatin, which has typically been viewed as a conformationally static entity. Our proof-of-concept study provides a powerful new methodology for studying nucleosome organization at a previously intractable resolution and offers up new avenues for modeling and visualizing higher order chromatin structure.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.