DNA-PK promotes DNA end resection at DNA double strand breaks in G0 cells

  1. Faith C Fowler
  2. Bo-Ruei Chen
  3. Nicholas Zolnerowich
  4. Wei Wu
  5. Raphael Pavani
  6. Jacob Paiano
  7. Chelsea Peart
  8. Zulong Chen
  9. André Nussenzweig
  10. Barry P Sleckman  Is a corresponding author
  11. Jessica K Tyler  Is a corresponding author
  1. Weill Cornell Medicine, United States
  2. University of Alabama at Birmingham, United States
  3. National Cancer Institute, United States

Abstract

DNA double-strand break (DSB) repair by homologous recombination is confined to the S and G2 phases of the cell cycle partly due to 53BP1 antagonizing DNA end resection in G1 phase and non-cycling quiescent (G0) cells where DSBs are predominately repaired by non-homologous end joining (NHEJ). Unexpectedly, we uncovered extensive MRE11- and CtIP-dependent DNA end resection at DSBs in G0 murine and human cells. A whole genome CRISPR/Cas9 screen revealed the DNA-dependent kinase (DNA-PK) complex as a key factor in promoting DNA end resection in G0 cells. In agreement, depletion of FBXL12, which promotes ubiquitylation and removal of the KU70/KU80 subunits of DNA-PK from DSBs, promotes even more extensive resection in G0 cells. In contrast, a requirement for DNA-PK in promoting DNA end resection in proliferating cells at the G1 or G2 phase of the cell cycle was not observed. Our findings establish that DNA-PK uniquely promotes DNA end resection in G0, but not in G1 or G2 phase cells, which has important implications for DNA DSB repair in quiescent cells.

Data availability

Sequencing data have been deposited in GEO under accession codesGSE186087

The following data sets were generated

Article and author information

Author details

  1. Faith C Fowler

    Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7180-8141
  2. Bo-Ruei Chen

    Department of Medicine, University of Alabama at Birmingham, Birmingham, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6404-2099
  3. Nicholas Zolnerowich

    Laboratory of Genome Integrity, National Cancer Institute, Bethesda, United States
    Competing interests
    No competing interests declared.
  4. Wei Wu

    Laboratory of Genome Integrity, National Cancer Institute, Bethesda, United States
    Competing interests
    No competing interests declared.
  5. Raphael Pavani

    Laboratory of Genome Integrity, National Cancer Institute, Bethesda, United States
    Competing interests
    No competing interests declared.
  6. Jacob Paiano

    Laboratory of Genome Integrity, National Cancer Institute, Bethesda, United States
    Competing interests
    No competing interests declared.
  7. Chelsea Peart

    Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, United States
    Competing interests
    No competing interests declared.
  8. Zulong Chen

    Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, United States
    Competing interests
    No competing interests declared.
  9. André Nussenzweig

    Laboratory of Genome Integrity, National Cancer Institute, Bethesda, United States
    Competing interests
    No competing interests declared.
  10. Barry P Sleckman

    Department of Medicine, University of Alabama at Birmingham, Birmingham, United States
    For correspondence
    bps@uab.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8295-4462
  11. Jessica K Tyler

    Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, United States
    For correspondence
    jet2021@med.cornell.edu
    Competing interests
    Jessica K Tyler, Senior editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9765-1659

Funding

NIH Office of the Director (R35 GM139816)

  • Jessica K Tyler

NIH Office of the Director (RO1 CA95641)

  • Jessica K Tyler

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

Reviewing Editor

  1. Wolf-Dietrich Heyer, University of California, Davis, United States

Version history

  1. Received: October 14, 2021
  2. Preprint posted: October 21, 2021 (view preprint)
  3. Accepted: May 6, 2022
  4. Accepted Manuscript published: May 16, 2022 (version 1)
  5. Version of Record published: May 20, 2022 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Metrics

  • 2,397
    views
  • 535
    downloads
  • 12
    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. Faith C Fowler
  2. Bo-Ruei Chen
  3. Nicholas Zolnerowich
  4. Wei Wu
  5. Raphael Pavani
  6. Jacob Paiano
  7. Chelsea Peart
  8. Zulong Chen
  9. André Nussenzweig
  10. Barry P Sleckman
  11. Jessica K Tyler
(2022)
DNA-PK promotes DNA end resection at DNA double strand breaks in G0 cells
eLife 11:e74700.
https://doi.org/10.7554/eLife.74700

Share this article

https://doi.org/10.7554/eLife.74700

Further reading

    1. Chromosomes and Gene Expression
    Rupam Choudhury, Anuroop Venkateswaran Venkatasubramani ... Axel Imhof
    Research Article

    Eukaryotic chromatin is organized into functional domains, that are characterized by distinct proteomic compositions and specific nuclear positions. In contrast to cellular organelles surrounded by lipid membranes, the composition of distinct chromatin domains is rather ill described and highly dynamic. To gain molecular insight into these domains and explore their composition, we developed an antibody-based proximity-biotinylation method targeting the RNA and proteins constituents. The method that we termed Antibody-Mediated-Proximity-Labelling-coupled to Mass Spectrometry (AMPL-MS) does not require the expression of fusion proteins and therefore constitutes a versatile and very sensitive method to characterize the composition of chromatin domains based on specific signature proteins or histone modifications. To demonstrate the utility of our approach we used AMPL-MS to characterize the molecular features of the chromocenter as well as the chromosome territory containing the hyperactive X-chromosome in Drosophila. This analysis identified a number of known RNA binding proteins in proximity of the hyperactive X and the centromere, supporting the accuracy of our method. In addition, it enabled us to characterize the role of RNA in the formation of these nuclear bodies. Furthermore, our method identified a new set of RNA molecules associated with the Drosophila centromere. Characterization of these novel molecules suggested the formation of R-loops in centromeres, which we validated using a novel probe for R-loops in Drosophila. Taken together, AMPL-MS improves the selectivity and specificity of proximity ligation allowing for novel discoveries of weak protein-RNA interactions in biologically diverse domains.

    1. Cancer Biology
    2. Chromosomes and Gene Expression
    Gregory Caleb Howard, Jing Wang ... William P Tansey
    Research Article

    The chromatin-associated protein WD Repeat Domain 5 (WDR5) is a promising target for cancer drug discovery, with most efforts blocking an arginine-binding cavity on the protein called the ‘WIN’ site that tethers WDR5 to chromatin. WIN site inhibitors (WINi) are active against multiple cancer cell types in vitro, the most notable of which are those derived from MLL-rearranged (MLLr) leukemias. Peptidomimetic WINi were originally proposed to inhibit MLLr cells via dysregulation of genes connected to hematopoietic stem cell expansion. Our discovery and interrogation of small-molecule WINi, however, revealed that they act in MLLr cell lines to suppress ribosome protein gene (RPG) transcription, induce nucleolar stress, and activate p53. Because there is no precedent for an anticancer strategy that specifically targets RPG expression, we took an integrated multi-omics approach to further interrogate the mechanism of action of WINi in human MLLr cancer cells. We show that WINi induce depletion of the stock of ribosomes, accompanied by a broad yet modest translational choke and changes in alternative mRNA splicing that inactivate the p53 antagonist MDM4. We also show that WINi are synergistic with agents including venetoclax and BET-bromodomain inhibitors. Together, these studies reinforce the concept that WINi are a novel type of ribosome-directed anticancer therapy and provide a resource to support their clinical implementation in MLLr leukemias and other malignancies.