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Updated: May 2, 2026

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
Published on: May 2, 2025
Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork
Constance Alabert1, Jimi-Carlo Bukowski-Wills2, Sung-Bau Lee1
1Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
This study reveals how proteins associate with DNA during replication using nascent chromatin capture. It maps protein dynamics, identifies new replication factors, and aids understanding of genome and epigenome maintenance.
Area of Science:
- Molecular Biology
- Genetics
- Cell Biology
Background:
- Genome stability relies on accurate DNA replication and chromatin duplication during cell division.
- Understanding the dynamic protein interactions during chromosome replication is crucial but challenging.
Purpose of the Study:
- To profile the dynamics of chromatin proteins during DNA replication in human cells.
- To identify proteins involved in nascent chromatin formation and their temporal association.
Main Methods:
- Nascent Chromatin Capture (NCC) technique involving biotin-dUTP labeling of replicating DNA.
- Affinity purification and quantitative proteomics to analyze protein association with nascent chromatin.
- Comparison of protein profiles between nascent and mature post-replicative chromatin.
Main Results:
- Detailed association dynamics for 3,995 proteins during replication.
- Identified enrichment of replication machinery and specific chromatin factors (e.g., CAF-1, DNMT1) in nascent chromatin.
- Observed delayed association of other factors (e.g., histone H1, PRC1) and correlated epigenetic modifications (H4K5K12diAc removal, H3K9me1 accumulation).
Conclusions:
- Provides a comprehensive resource for understanding genome and epigenome maintenance during replication.
- Identified 93 uncharacterized proteins with predicted roles in nascent chromatin.
- Discovered FAM111A as a novel replication factor essential for PCNA loading.
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