1. Genetics and Genomics
  2. Microbiology and Infectious Disease

Herpesviral lytic gene functions render the viral genome susceptible to novel editing by CRISPR/Cas9

  1. Hyung Suk Oh
  2. Werner M Neuhausser  Is a corresponding author
  3. Pierce Eggan
  4. Magdalena Angelova
  5. Rory Kirchner
  6. Kevin C Eggan
  7. David M Knipe  Is a corresponding author
  1. Harvard Medical School, United States
  2. Harvard University, United States
  3. Harvard T H Chan School of Public Health, United States
https://doi.org/10.7554/eLife.51662
Share this article
Cite this article
  1. Hyung Suk Oh
  2. Werner M Neuhausser
  3. Pierce Eggan
  4. Magdalena Angelova
  5. Rory Kirchner
  6. Kevin C Eggan
  7. David M Knipe
(2019)
Herpesviral lytic gene functions render the viral genome susceptible to novel editing by CRISPR/Cas9
eLife 8:e51662.
https://doi.org/10.7554/eLife.51662
  2. Download BibTeX
  3. Download .RIS

Abstract

Herpes simplex virus (HSV) establishes lifelong latent infection and can cause serious human disease, but current antiviral therapies target lytic but not latent infection. We screened for sgRNAs that cleave HSV-1 DNA sequences efficiently in vitro and used these sgRNAs to observe the first editing of quiescent HSV-1 DNA. The sgRNAs targeted lytic replicating viral DNA genomes more efficiently than quiescent genomes, consistent with the open structure of lytic chromatin. Editing of latent genomes caused short indels while editing of replicating genomes produced indels, linear molecules and large genomic sequence loss around the gRNA target site. The HSV ICP0 protein and viral DNA replication increased the loss of DNA sequences around the gRNA target site. We conclude that HSV, by promoting open chromatin needed for viral gene expression and by inhibiting the DNA damage response, makes the genome vulnerable to a novel form of editing by CRISPR-Cas9 during lytic replication.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files.

The following previously published data sets were used
    1. Miga KH
    2. Newton Y
    3. Jain M
    4. Altemose N
    5. Willard HF
    6. Kent WJ
    (2014) hg38
    Genome Reference Consortium, Human GRCh38.p12 (GCA_000001405.27).
    https://genome.ucsc.edu/cgi-bin/hgGateway?db=hg38

Article and author information

Author details

  1. Hyung Suk Oh

    Department of Microbiology, Harvard Medical School, Boston, United States
    Competing interests
    Hyung Suk Oh, We have patent applications pending. U.S. Patent application No. 62/365,826, International Patent Application PCT/US2017/043225.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1739-0389

  2. Werner M Neuhausser

    Department of Obstetrics and Gynecology, Harvard Medical School, Boston, United States
    For correspondence
    wneuhaus@bidmc.harvard.edu
    Competing interests
    Werner M Neuhausser, We have patent applications pending. U.S. Patent application No. 62/365,826, International Patent Application PCT/US2017/043225.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5092-2658

  3. Pierce Eggan

    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
    Competing interests
    No competing interests declared.

  4. Magdalena Angelova

    Department of Microbiology, Harvard Medical School, Boston, United States
    Competing interests
    Magdalena Angelova, We have patent applications pending. U.S. Patent application No. 62/365,826, International Patent Application PCT/US2017/043225.

  5. Rory Kirchner

    Department of Biostatistics, Harvard T H Chan School of Public Health, Boston, United States
    Competing interests
    No competing interests declared.

  6. Kevin C Eggan

    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
    Competing interests
    Kevin C Eggan, We have patent applications pending. U.S. Patent application No. 62/365,826, International Patent Application PCT/US2017/043225.

  7. David M Knipe

    Department of Microbiology, Harvard Medical School, Boston, United States
    For correspondence
    david_knipe@hms.harvard.edu
    Competing interests
    David M Knipe, Reviewing editor, eLifeWe have patent applications pending. U.S. Patent application No. 62/365,826, International Patent Application PCT/US2017/043225.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1554-6236

Funding

National Institutes of Health (P01 AI098681)

  • David M Knipe

National Institutes of Health (R21 AI135423)

  • Kevin C Eggan

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

Copyright

© 2019, Oh 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.

Metrics

  • 7,582
    views
  • 538
    downloads
  • 32
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Hyung Suk Oh
  2. Werner M Neuhausser
  3. Pierce Eggan
  4. Magdalena Angelova
  5. Rory Kirchner
  6. Kevin C Eggan
  7. David M Knipe
(2019)
Herpesviral lytic gene functions render the viral genome susceptible to novel editing by CRISPR/Cas9
eLife 8:e51662.
https://doi.org/10.7554/eLife.51662

Share this article

https://doi.org/10.7554/eLife.51662

Categories and tags

Research organism

Further reading

    1. Cell Biology
    2. Genetics and Genomics

    Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress

    Showkat Ahmad Dar, Sulochan Malla ... Manolis Maragkakis
    Research Article

    Cells react to stress by triggering response pathways, leading to extensive alterations in the transcriptome to restore cellular homeostasis. The role of RNA metabolism in shaping the cellular response to stress is vital, yet the global changes in RNA stability under these conditions remain unclear. In this work, we employ direct RNA sequencing with nanopores, enhanced by 5ʹ end adapter ligation, to comprehensively interrogate the human transcriptome at single-molecule and -nucleotide resolution. By developing a statistical framework to identify robust RNA length variations in nanopore data, we find that cellular stress induces prevalent 5ʹ end RNA decay that is coupled to translation and ribosome occupancy. Unlike typical RNA decay models in normal conditions, we show that stress-induced RNA decay is dependent on XRN1 but does not depend on deadenylation or decapping. We observed that RNAs undergoing decay are predominantly enriched in the stress granule transcriptome while inhibition of stress granule formation via genetic ablation of G3BP1 and G3BP2 rescues RNA length. Our findings reveal RNA decay as a key component of RNA metabolism upon cellular stress that is dependent on stress granule formation.

    1. Genetics and Genomics
    2. Neuroscience

    Statistical examination of shared loci in neuropsychiatric diseases using genome-wide association study summary statistics

    Thomas P Spargo, Lachlan Gilchrist ... Alfredo Iacoangeli
    Research Article

    Continued methodological advances have enabled numerous statistical approaches for the analysis of summary statistics from genome-wide association studies. Genetic correlation analysis within specific regions enables a new strategy for identifying pleiotropy. Genomic regions with significant ‘local’ genetic correlations can be investigated further using state-of-the-art methodologies for statistical fine-mapping and variant colocalisation. We explored the utility of a genome-wide local genetic correlation analysis approach for identifying genetic overlaps between the candidate neuropsychiatric disorders, Alzheimer’s disease (AD), amyotrophic lateral sclerosis (ALS), frontotemporal dementia, Parkinson’s disease, and schizophrenia. The correlation analysis identified several associations between traits, the majority of which were loci in the human leukocyte antigen region. Colocalisation analysis suggested that disease-implicated variants in these loci often differ between traits and, in one locus, indicated a shared causal variant between ALS and AD. Our study identified candidate loci that might play a role in multiple neuropsychiatric diseases and suggested the role of distinct mechanisms across diseases despite shared loci. The fine-mapping and colocalisation analysis protocol designed for this study has been implemented in a flexible analysis pipeline that produces HTML reports and is available at: https://github.com/ThomasPSpargo/COLOC-reporter.

    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

    Arkadiy K Golov, Alexey A Gavrilov ... Sergey V Razin
    Research Article

    The enhancer-promoter looping model, in which enhancers activate their target genes via physical contact, has long dominated the field of gene regulation. However, the ubiquity of this model has been questioned due to evidence of alternative mechanisms and the lack of its systematic validation, primarily owing to the absence of suitable experimental techniques. In this study, we present a new MNase-based proximity ligation method called MChIP-C, allowing for the measurement of protein-mediated chromatin interactions at single-nucleosome resolution on a genome-wide scale. By applying MChIP-C to study H3K4me3 promoter-centered interactions in K562 cells, we found that it had greatly improved resolution and sensitivity compared to restriction endonuclease-based C-methods. This allowed us to identify EP300 histone acetyltransferase and the SWI/SNF remodeling complex as potential candidates for establishing and/or maintaining enhancer-promoter interactions. Finally, leveraging data from published CRISPRi screens, we found that most functionally verified enhancers do physically interact with their cognate promoters, supporting the enhancer-promoter looping model.