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

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

doi:10.1038/ncb2918

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

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

188 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 language	English
Journal	Nature Cell Biology
ISSN	1465-7392
DOIs	https://doi.org/10.1038/ncb2918
Publication status	Published - Mar 2014

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@article{d0906b76ae284a42aca4f3549837bc0e,

title = "Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components",

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.",

author = "Constance Alabert and Jimi-Carlo Bukowski-Wills and Sung-Po Lee and Georg Kustatscher and Kyosuke Nakamura and {de Lima Alves}, Flavia and Patrice Menard and Jakob Mejlvang and Juri Rappsilber and Anja Groth",

year = "2014",

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doi = "10.1038/ncb2918",

language = "English",

journal = "Nature Cell Biology",

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T1 - Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components

AU - Alabert, Constance

AU - Bukowski-Wills, Jimi-Carlo

AU - Lee, Sung-Po

AU - Kustatscher, Georg

AU - Nakamura, Kyosuke

AU - de Lima Alves, Flavia

AU - Menard, Patrice

AU - Mejlvang, Jakob

AU - Rappsilber, Juri

AU - Groth, Anja

PY - 2014/3

Y1 - 2014/3

N2 - 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.

AB - 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.

U2 - 10.1038/ncb2918

DO - 10.1038/ncb2918

M3 - Journal article

C2 - 24561620

SN - 1465-7392

JO - Nature Cell Biology

JF - Nature Cell Biology

ER -

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

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