ArticleCell2025
The single-molecule accessibility landscape of newly replicated mammalian chromatin.
Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- A practical guide to studying genome function using single-molecule genomics.Nature reviews. Molecular cell biology · 2026Review
- Newly synthesized histones: passive or active players in the regulation of epigenetic inheritance?Nucleic acids research · 2026Review
- Spatial organization and dynamics of genome replication: from forks to foci.Nucleic acids research · 2026Review
- Single-molecule nucleosome spacing coordinates chromatin fiber interactions.bioRxiv : the preprint server for biology · 2026Article
- Article
- Post-replicative chromatin accessibility predicts cell fate change.Stem cell reports · 2026Article
- Genome-wide classification of tumor-derived reads from bulk long-read sequencing.bioRxiv : the preprint server for biology · 2026Article
- CTCF/cohesin-binding sites are susceptible to replication-associated DNA damage and genomic instability in cancer cells.iScience · 2026Article
- 3D genome folding in epigenetic regulation and cellular memory.Trends in cell biology · 2026Review
- Article
- Nascent CUT&Tag captures transcription factor binding after chromatin duplication.bioRxiv : the preprint server for biology · 2025Article
- The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers.bioRxiv : the preprint server for biology · 2025Article
- Phasing single-molecule nano-NOMe-seq reveals chromatin state heterogeneity in the context of transcription and long-range interactions.bioRxiv : the preprint server for biology · 2025Article
- Bicoid-nucleosome competition sets a concentration threshold for transcription constrained by genome replication.Cell reports · 2025Article
- Beyond genomic weaving: molecular roles for CTCF outside cohesin loop extrusion.Current opinion in genetics & development · 2025Review
- Telomere-to-telomere DNA replication timing profiling using single-molecule sequencing with Nanotiming.Nature communications · 2025Article
- Monitoring and quantifying replication fork dynamics with high-throughput methods.Communications biology · 2024Review
- Acute multi-level response to defectivebioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
We present replication-aware single-molecule accessibility mapping (RASAM), a method to nondestructively measure replication status and protein-DNA interactions on chromatin genome-wide. Using RASAM, we uncover a genome-wide state of single-molecule "hyperaccessibility" post-replication that resolves over several hours. Combining RASAM with cellular models for rapid protein degradation, we demonstrate that histone chaperone CAF-1 reduces nascent chromatin accessibility by filling single-molecular "gaps" and generating closely spaced dinucleosomes on replicated DNA. At cis-regulatory elements, we observe unique modes by which nascent chromatin hyperaccessibility resolves: at CCCTC-binding factor (CTCF)-binding sites, CTCF and nucleosomes compete, reducing CTCF occupancy and motif accessibility post-replication; at active transcription start sites, high chromatin accessibility is maintained, implying rapid re-establishment of nucleosome-free regions. Our study introduces a new paradigm for studying replicated chromatin fiber organization. More broadly, we uncover a unique organization of newly replicated chromatin that must be reset by active processes, providing a substrate for epigenetic reprogramming.
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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.