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Proteomic profiling reveals distinct phases to the restoration of chromatin following DNA replication

ABSTRACT: Chromatin organization must be maintained during cell proliferation to preserve cellular identity and genome integrity. However, DNA replication results in transient displacement of DNA bound proteins, and it is unclear how they regain access to newly replicated DNA. Using quantitative MS-based proteomics coupled to isolation of proteins on nascent DNA (iPOND), we provide time resolved binding kinetics for thousands of proteins behind replisomes in the lung fibroblast cell line TIG-3 (JCRB0506, JCRB Cell Bank). Performing hierarchical clustering, we identified four groups of protein behaviour: Transient enriched on nascent, restored within 11min, peaking in G2/M, and delayed restored. Overall, our data show that most proteins (85%) regain access within the first 2h after the passage of the fork. Only a small percentage of proteins is restored after 2h post-replication, with 5.3 % of factors peaking in G2/M and 9.1% factors not restored before the next G1 phase. We provide evidence that DNA replication not only disrupts but also promotes recruitment of transcription factors and chromatin remodelers, providing a significant advance in understanding how DNA replication could contribute to programmed changes of cell memory.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Vanesa Alvarez

LAB HEAD: Constance Alabert

PROVIDER: PXD036236 | Pride | 2023-02-02

REPOSITORIES: Pride

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			Action	DRS
	Data_information.xlsx	Xlsx
	Homo_sapiens_SpTr_canonical_20190902.fasta	Fasta
	IP_combined.zip	Other
	Input_combined.zip	Other
	Input_mqpar.xml	Xml

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Proteomic profiling reveals distinct phases to the restoration of chromatin following DNA replication

Project description:Chromatin organization must be maintained during cell proliferation to preserve cellular identity and genome integrity. However, DNA replication results in transient displacement of DNA bound proteins, and it is unclear how they regain access to newly replicated DNA. Using quantitative MS-based proteomics coupled to Nascent Chromatin Capture, we provide time resolved binding kinetics for thousands of proteins behind replisomes of mid-S replicated regions. This shows that most proteins regain access within the first 15 minutes after the passage of the fork. In contrast, 25% of the identified proteins do not, and this delay cannot be inferred from their known function, physicochemical properties, or nuclear abundance. A sample treated with nocodazole to block the cell cycle progression. The comparison between a normal cell cycle progression and a nocodazole treated sample shows that the reassociation onto chromatin of proteins with a delayed restoration can be regulated by the cell cycle progression and/or the post-replication time. In addition, we provide evidence that DNA replication not only disrupts but also promotes recruitment of transcription factors and chromatin remodellers, providing a significant advance in understanding how DNA replication could contribute to programmed changes of cell memory. Data available in this entry are related with the supplementary table 5 from our manuscript.

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Proteomic profiling reveals distinct phases to the restoration of chromatin following DNA replication

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