The single-molecule accessibility landscape of newly replicated mammalian chromatin
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.
Authors
- Emily V. Wong (ORCID: https://orcid.org/0000-0001-5582-6043)
- Vijay Ramani (ORCID: https://orcid.org/0000-0003-3345-5960)
- Isha H. Jain (ORCID: https://orcid.org/0000-0001-5053-0964)
- Nour J. Abdulhay
- Simai Wang (ORCID: https://orcid.org/0009-0005-2292-6116)
- Iryna Irkliyenko (ORCID: https://orcid.org/0000-0002-3027-1632)
- Brandon T.L. Chew (ORCID: https://orcid.org/0000-0002-6639-3113)
- Elphège P. Nora (ORCID: https://orcid.org/0000-0002-8347-4396)
- Anja Groth (ORCID: https://orcid.org/0000-0003-0577-1771)
- Alva Biran (ORCID: https://orcid.org/0000-0002-0276-2004)
- Megan S Ostrowski (ORCID: https://orcid.org/0000-0001-9845-9319)
- Hani Goodarzi (ORCID: https://orcid.org/0000-0002-9648-8949)
- Marty G. Yang (ORCID: https://orcid.org/0000-0001-5788-3092)
- Colin P McNally (ORCID: https://orcid.org/0000-0002-2169-5302)
- Jonathan Sandoval
- Ayush D Midha
- Keerthi Renduchintala
Institutions
- University of Copenhagen (DK)
- Gladstone Institutes (US)
- University of California, San Francisco (US)
- Novo Nordisk Foundation (DK)
- Czech Academy of Sciences, Institute of Biophysics (CZ)
- Chan Zuckerberg Initiative (United States) (US)
- UCSF Helen Diller Family Comprehensive Cancer Center (US)
Publication Details
- Journal
- Cell
- Published
- 2024-11-15
- DOI
- https://doi.org/10.1016/j.cell.2024.10.039
- Citations
- 24
- Primary Topic
- Genomics and Chromatin Dynamics
- Type
- article
- Field-Weighted Citation Impact
- 5.38
Funders
- Gladstone Institutes
- University of Pittsburgh
- University of California, San Francisco
- National Human Genome Research Institute