Temporal profiling of the chromatin proteome reveals system-wide responses to replication inhibition

Guennadi A. Khoudoli, Peter J. Gillespie, Graeme Stewart, Jens S. Andersen, Jason R. Swedlow (Lead / Corresponding author), J. Julian Blow (Lead / Corresponding author)

    Research output: Contribution to journalArticle

    26 Citations (Scopus)

    Abstract

    Although the replication, expression, and maintenance of DNA are well-studied processes, the way that they are coordinated is poorly understood. Here, we report an analysis of the changing association of proteins with chromatin (the chromatin proteome) during progression through interphase of the cell cycle. Sperm nuclei were incubated in Xenopus egg extracts, and chromatin-associated proteins were analyzed by mass spectrometry at different times. Approximately 75% of the proteins varied in abundance on chromatin by more than 15%, suggesting that the chromatin proteome is highly dynamic. Proteins were then assigned to one of 12 different clusters on the basis of their pattern of chromatin association. Each cluster contained functional groups of proteins involved in different nuclear processes related to progression through interphase. We also blocked DNA replication by inhibiting either replication licensing or S phase CDK activity. This revealed an unexpectedly broad system-wide effect on the chromatin proteome, indicating that the response to replication inhibition extends to many other functional modules in addition to the replication machinery. Several proteins that respond to replication inhibition (including nuclear pore proteins) coprecipitated with the Mcm2-7 licensing complex on chromatin, suggesting that Mcm2-7 play a central role in coordinating nuclear structure with DNA replication.

    Original languageEnglish
    Pages (from-to)838-843
    Number of pages6
    JournalCurrent Biology
    Volume18
    Issue number11
    DOIs
    Publication statusPublished - 3 Jun 2008

    Keywords

    • DNA-REPLICATION
    • CELL-DIVISION
    • REMODELING COMPLEX
    • CHROMOSOMAL DNA
    • PROTEINS
    • XENOPUS
    • DYNAMICS
    • GEMININ
    • CYCLE

    Cite this

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    title = "Temporal profiling of the chromatin proteome reveals system-wide responses to replication inhibition",
    abstract = "Although the replication, expression, and maintenance of DNA are well-studied processes, the way that they are coordinated is poorly understood. Here, we report an analysis of the changing association of proteins with chromatin (the chromatin proteome) during progression through interphase of the cell cycle. Sperm nuclei were incubated in Xenopus egg extracts, and chromatin-associated proteins were analyzed by mass spectrometry at different times. Approximately 75{\%} of the proteins varied in abundance on chromatin by more than 15{\%}, suggesting that the chromatin proteome is highly dynamic. Proteins were then assigned to one of 12 different clusters on the basis of their pattern of chromatin association. Each cluster contained functional groups of proteins involved in different nuclear processes related to progression through interphase. We also blocked DNA replication by inhibiting either replication licensing or S phase CDK activity. This revealed an unexpectedly broad system-wide effect on the chromatin proteome, indicating that the response to replication inhibition extends to many other functional modules in addition to the replication machinery. Several proteins that respond to replication inhibition (including nuclear pore proteins) coprecipitated with the Mcm2-7 licensing complex on chromatin, suggesting that Mcm2-7 play a central role in coordinating nuclear structure with DNA replication.",
    keywords = "DNA-REPLICATION, CELL-DIVISION, REMODELING COMPLEX, CHROMOSOMAL DNA, PROTEINS, XENOPUS, DYNAMICS, GEMININ, CYCLE",
    author = "Khoudoli, {Guennadi A.} and Gillespie, {Peter J.} and Graeme Stewart and Andersen, {Jens S.} and Swedlow, {Jason R.} and Blow, {J. Julian}",
    year = "2008",
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    Temporal profiling of the chromatin proteome reveals system-wide responses to replication inhibition. / Khoudoli, Guennadi A.; Gillespie, Peter J.; Stewart, Graeme; Andersen, Jens S.; Swedlow, Jason R. (Lead / Corresponding author); Blow, J. Julian (Lead / Corresponding author).

    In: Current Biology, Vol. 18, No. 11, 03.06.2008, p. 838-843.

    Research output: Contribution to journalArticle

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    AU - Khoudoli, Guennadi A.

    AU - Gillespie, Peter J.

    AU - Stewart, Graeme

    AU - Andersen, Jens S.

    AU - Swedlow, Jason R.

    AU - Blow, J. Julian

    PY - 2008/6/3

    Y1 - 2008/6/3

    N2 - Although the replication, expression, and maintenance of DNA are well-studied processes, the way that they are coordinated is poorly understood. Here, we report an analysis of the changing association of proteins with chromatin (the chromatin proteome) during progression through interphase of the cell cycle. Sperm nuclei were incubated in Xenopus egg extracts, and chromatin-associated proteins were analyzed by mass spectrometry at different times. Approximately 75% of the proteins varied in abundance on chromatin by more than 15%, suggesting that the chromatin proteome is highly dynamic. Proteins were then assigned to one of 12 different clusters on the basis of their pattern of chromatin association. Each cluster contained functional groups of proteins involved in different nuclear processes related to progression through interphase. We also blocked DNA replication by inhibiting either replication licensing or S phase CDK activity. This revealed an unexpectedly broad system-wide effect on the chromatin proteome, indicating that the response to replication inhibition extends to many other functional modules in addition to the replication machinery. Several proteins that respond to replication inhibition (including nuclear pore proteins) coprecipitated with the Mcm2-7 licensing complex on chromatin, suggesting that Mcm2-7 play a central role in coordinating nuclear structure with DNA replication.

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