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Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes

Author

Listed:
  • Benjamin M. Spector

    (The University of Iowa)

  • Mrutyunjaya Parida

    (The University of Iowa)

  • Ming Li

    (The University of Iowa
    The University of Iowa
    The University of Iowa
    Veterans Affairs Health Care System)

  • Christopher B. Ball

    (The University of Iowa)

  • Jeffery L. Meier

    (The University of Iowa
    The University of Iowa
    Veterans Affairs Health Care System)

  • Donal S. Luse

    (Lerner Research Institute, Cleveland Clinic)

  • David H. Price

    (The University of Iowa)

Abstract

Interactions of the RNA polymerase II (Pol II) preinitiation complex (PIC) and paused early elongation complexes with the first downstream (+1) nucleosome are thought to be functionally important. However, current methods are limited for investigating these relationships, both for cellular chromatin and the human cytomegalovirus (HCMV) genome. Digestion with human DNA fragmentation factor (DFF) before immunoprecipitation (DFF-ChIP) precisely revealed both similarities and major differences in PICs driven by TBP on the host genome in comparison with PICs driven by TBP or the viral-specific, late initiation factor UL87 on the viral genome. Host PICs and paused Pol II complexes are frequently found in contact with the +1 nucleosome and paused Pol II can also be found in a complex involved in the initial invasion of the +1 nucleosome. In contrast, viral transcription complexes have very limited nucleosomal interactions, reflecting a relative lack of chromatinization of transcriptionally active regions of HCMV genomes.

Suggested Citation

  • Benjamin M. Spector & Mrutyunjaya Parida & Ming Li & Christopher B. Ball & Jeffery L. Meier & Donal S. Luse & David H. Price, 2022. "Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29739-x
    DOI: 10.1038/s41467-022-29739-x
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    References listed on IDEAS

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