Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components

Constance Alabert, Jimi-Carlo Bukowski-Wills, Sung-Bau Lee, Georg Kustatscher, Kyosuke Nakamura, Flavia de Lima Alves, Patrice Menard, Jakob Mejlvang, Juri Rappsilber, Anja Groth

Research output: Contribution to journalArticle

147 Citations (Scopus)

Abstract

To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use nascent chromatin capture (NCC) to profile chromatin proteome dynamics during replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3,995 proteins. The replication machinery and 485 chromatin factors such as CAF-1, DNMT1 and SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, whereas H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC enrichment with experimentally derived chromatin probabilities to predict a function in nascent chromatin for 93 uncharacterized proteins, and identify FAM111A as a replication factor required for PCNA loading. Together, this provides an extensive resource to understand genome and epigenome maintenance.

Original languageEnglish
Pages (from-to)281-93
Number of pages13
JournalNature Cell Biology
Volume16
Issue number3
DOIs
Publication statusPublished - Feb 23 2014
Externally publishedYes

Fingerprint

DNA Replication
Proteomics
Chromatin
Genomic Instability
Proliferating Cell Nuclear Antigen
Proteome
Biotin
Cell Division
Histones
Proteins
Chromosomes
Maintenance
Genome
DNA

Keywords

  • Chromatin
  • Chromatin Assembly and Disassembly
  • Chromosomal Proteins, Non-Histone
  • DNA Replication
  • DNA-Binding Proteins
  • HeLa Cells
  • Histones
  • Humans
  • Proliferating Cell Nuclear Antigen
  • Protein Transport
  • Proteome
  • Proteomics
  • Receptors, Virus
  • S Phase Cell Cycle Checkpoints
  • Journal Article
  • Research Support, Non-U.S. Gov't

Cite this

Alabert, C., Bukowski-Wills, J-C., Lee, S-B., Kustatscher, G., Nakamura, K., de Lima Alves, F., ... Groth, A. (2014). Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components. Nature Cell Biology, 16(3), 281-93. https://doi.org/10.1038/ncb2918

Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components. / Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Bau; Kustatscher, Georg; Nakamura, Kyosuke; de Lima Alves, Flavia; Menard, Patrice; Mejlvang, Jakob; Rappsilber, Juri; Groth, Anja.

In: Nature Cell Biology, Vol. 16, No. 3, 23.02.2014, p. 281-93.

Research output: Contribution to journalArticle

Alabert, C, Bukowski-Wills, J-C, Lee, S-B, Kustatscher, G, Nakamura, K, de Lima Alves, F, Menard, P, Mejlvang, J, Rappsilber, J & Groth, A 2014, 'Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components', Nature Cell Biology, vol. 16, no. 3, pp. 281-93. https://doi.org/10.1038/ncb2918
Alabert, Constance ; Bukowski-Wills, Jimi-Carlo ; Lee, Sung-Bau ; Kustatscher, Georg ; Nakamura, Kyosuke ; de Lima Alves, Flavia ; Menard, Patrice ; Mejlvang, Jakob ; Rappsilber, Juri ; Groth, Anja. / Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components. In: Nature Cell Biology. 2014 ; Vol. 16, No. 3. pp. 281-93.
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