A CRISPR-based rapid DNA repositioning strategy and the early intranuclear life of HSV-1

  1. Juan Xiang
  2. Zhaoyang Fan
  3. Hongchang Dong
  4. Yilei Ma
  5. Pei Xu  Is a corresponding author
  1. Sun Yat-sen University, China

Abstract

The relative positions of viral DNA genomes to the host intranuclear environment play critical roles in determining virus fate. Recent advances in the application of chromosome conformation capture-based sequencing analysis (3C technologies) have revealed valuable aspects of the spatiotemporal interplay of viral genomes with host chromosomes. However, to elucidate the causal relationship between the subnuclear localization of viral genomes and the pathogenic outcome of an infection, manipulative tools are needed. Rapid repositioning of viral DNAs to specific subnuclear compartments amid infection is a powerful approach to synchronize and interrogate this dynamically changing process in space and time. Herein, we report an inducible CRISPR-based two-component platform that relocates extrachromosomal DNA pieces (5 kb to 170 kb) to the nuclear periphery in minutes (CRISPR-nuPin). Based on this strategy, investigations of herpes simplex virus 1 (HSV-1), a prototypical member of the human herpesvirus family, revealed unprecedently reported insights into the early intranuclear life of the pathogen: I) Viral genomes tethered to the nuclear periphery upon entry, compared with those freely infecting the nucleus, were wrapped around histones with increased suppressive modifications and subjected to stronger transcriptional silencing and prominent growth inhibition. II) Relocating HSV-1 genomes at 1 hour post infection significantly promoted the transcription of viral genes, termed an 'Escaping' effect. III) Early accumulation of ICP0 was a sufficient but not necessary condition for 'Escaping'. IV) Subnuclear localization was only critical during early infection. Importantly, the CRISPR-nuPin tactic, in principle, is applicable to many other DNA viruses.

Data availability

No datasets and code were generated or used during the study. All raw microscopy images, original files for charts and blots on Dryad.

The following data sets were generated

Article and author information

Author details

  1. Juan Xiang

    The Centre for Infection and Immunity Studies, Sun Yat-sen University, Guangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  2. Zhaoyang Fan

    The Centre for Infection and Immunity Studies, Sun Yat-sen University, Guangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2286-4865
  3. Hongchang Dong

    The Centre for Infection and Immunity Studies, Sun Yat-sen University, Guangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  4. Yilei Ma

    The Centre for Infection and Immunity Studies, Sun Yat-sen University, Guangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  5. Pei Xu

    The Centre for Infection and Immunity Studies, Sun Yat-sen University, Guangzhou, China
    For correspondence
    xupei3@mail.sysu.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2719-5605

Funding

National Key Research and Development Program of China (2022YFC2305400)

  • Pei Xu

National Natural Science Foundation of China (No. 31870157)

  • Pei Xu

Shenzhen Science and Technology Innovation Program (JCYJ20180307151536743)

  • Pei Xu

Shenzhen Science and Technology Innovation Program (KQTD20180411143323605)

  • Pei Xu

Natural Science Foundation of Shenzhen Municipality (JCYJ2022050145810023)

  • Pei Xu

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Karla Kirkegaard, Stanford University School of Medicine, United States

Version history

  1. Preprint posted: April 8, 2022 (view preprint)
  2. Received: December 6, 2022
  3. Accepted: September 12, 2023
  4. Accepted Manuscript published: September 13, 2023 (version 1)
  5. Version of Record published: September 26, 2023 (version 2)

Copyright

© 2023, Xiang et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Juan Xiang
  2. Zhaoyang Fan
  3. Hongchang Dong
  4. Yilei Ma
  5. Pei Xu
(2023)
A CRISPR-based rapid DNA repositioning strategy and the early intranuclear life of HSV-1
eLife 12:e85412.
https://doi.org/10.7554/eLife.85412

Share this article

https://doi.org/10.7554/eLife.85412

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