1. Chromosomes and Gene Expression
  2. Structural Biology and Molecular Biophysics

CtIP forms a tetrameric dumbbell-shaped particle which bridges complex DNA end structures for double-strand break repair

  1. Oliver J Wilkinson
  2. Alejandro Martín-González
  3. Haejoo Kang
  4. Sarah J Northall
  5. Dale B Wigley
  6. Fernando Moreno-Herrero
  7. Mark Simon Dillingham  Is a corresponding author
  1. University of Bristol, United Kingdom
  2. Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Spain
  3. Imperial College London, United Kingdom
https://doi.org/10.7554/eLife.42129
Share this article
Cite this article
  1. Oliver J Wilkinson
  2. Alejandro Martín-González
  3. Haejoo Kang
  4. Sarah J Northall
  5. Dale B Wigley
  6. Fernando Moreno-Herrero
  7. Mark Simon Dillingham
(2019)
CtIP forms a tetrameric dumbbell-shaped particle which bridges complex DNA end structures for double-strand break repair
eLife 8:e42129.
https://doi.org/10.7554/eLife.42129
  2. Download BibTeX
  3. Download .RIS

Abstract

CtIP is involved in the resection of broken DNA during the S and G2 phases of the cell cycle for repair by recombination. Acting with the MRN complex, it plays a particularly important role in handling complex DNA end structures by localised nucleolytic processing of DNA termini in preparation for longer range resection. Here we show that human CtIP is a tetrameric protein adopting a dumbbell architecture in which DNA binding domains are connected by long coiled-coils. The protein complex binds two short DNA duplexes with high affinity and bridges DNA molecules in trans. DNA binding is potentiated by dephosphorylation and is not specific for DNA end structures per se. However, the affinity for linear DNA molecules is increased if the DNA terminates with complex structures including forked ssDNA overhangs and nucleoprotein conjugates. This work provides a biochemical and structural basis for the function of CtIP at complex DNA breaks.

Data availability

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

Article and author information

Author details

  1. Oliver J Wilkinson

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  2. Alejandro Martín-González

    Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.

  3. Haejoo Kang

    Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  4. Sarah J Northall

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  5. Dale B Wigley

    Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0786-6726

  6. Fernando Moreno-Herrero

    Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4083-1709

  7. Mark Simon Dillingham

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    For correspondence
    mark.dillingham@bristol.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4612-7141

Funding

Wellcome (100401/Z/12/Z)

  • Oliver J Wilkinson
  • Sarah J Northall
  • Mark Simon Dillingham

Cancer Research UK (C6913/A21608)

  • Haejoo Kang
  • Dale B Wigley

Spanish Ministry of Science (BFU2017-83794-P)

  • Fernando Moreno-Herrero

European Research Council (681299)

  • Fernando Moreno-Herrero

Spanish MINECO (BES-2015-071244)

  • Alejandro Martín-González

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

Reviewing Editor

  1. Maria Spies, University of Iowa, United States

Version history

  1. Received: September 19, 2018
  2. Accepted: January 1, 2019
  3. Accepted Manuscript published: January 2, 2019 (version 1)
  4. Version of Record published: January 23, 2019 (version 2)

Copyright

© 2019, Wilkinson 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

  • 3,985
    Page views
  • 548
    Downloads
  • 17
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

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. Oliver J Wilkinson
  2. Alejandro Martín-González
  3. Haejoo Kang
  4. Sarah J Northall
  5. Dale B Wigley
  6. Fernando Moreno-Herrero
  7. Mark Simon Dillingham
(2019)
CtIP forms a tetrameric dumbbell-shaped particle which bridges complex DNA end structures for double-strand break repair
eLife 8:e42129.
https://doi.org/10.7554/eLife.42129

Categories and tags

Research organism

Further reading

    1. Chromosomes and Gene Expression
    2. Neuroscience

    Avoiding false discoveries in single-cell RNA-seq by revisiting the first Alzheimer’s disease dataset

    Alan E Murphy, Nurun Fancy, Nathan Skene
    Research Article

    Mathys et al. conducted the first single-nucleus RNA-seq (snRNA-seq) study of Alzheimer’s disease (AD) (Mathys et al., 2019). With bulk RNA-seq, changes in gene expression across cell types can be lost, potentially masking the differentially expressed genes (DEGs) across different cell types. Through the use of single-cell techniques, the authors benefitted from increased resolution with the potential to uncover cell type-specific DEGs in AD for the first time. However, there were limitations in both their data processing and quality control and their differential expression analysis. Here, we correct these issues and use best-practice approaches to snRNA-seq differential expression, resulting in 549 times fewer DEGs at a false discovery rate of 0.05. Thus, this study highlights the impact of quality control and differential analysis methods on the discovery of disease-associated genes and aims to refocus the AD research field away from spuriously identified genes.

    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Chromosome-specific maturation of the epigenome in the Drosophila male germline

    James T Anderson, Steven Henikoff, Kami Ahmad
    Research Article

    Spermatogenesis in the Drosophila male germline proceeds through a unique transcriptional program controlled both by germline-specific transcription factors and by testis-specific versions of core transcriptional machinery. This program includes the activation of genes on the heterochromatic Y chromosome, and reduced transcription from the X chromosome, but how expression from these sex chromosomes is regulated has not been defined. To resolve this, we profiled active chromatin features in the testes from wildtype and meiotic arrest mutants and integrate this with single-cell gene expression data from the Fly Cell Atlas. These data assign the timing of promoter activation for genes with germline-enriched expression throughout spermatogenesis, and general alterations of promoter regulation in germline cells. By profiling both active RNA polymerase II and histone modifications in isolated spermatocytes, we detail widespread patterns associated with regulation of the sex chromosomes. Our results demonstrate that the X chromosome is not enriched for silencing histone modifications, implying that sex chromosome inactivation does not occur in the Drosophila male germline. Instead, a lack of dosage compensation in spermatocytes accounts for the reduced expression from this chromosome. Finally, profiling uncovers dramatic ubiquitinylation of histone H2A and lysine-16 acetylation of histone H4 across the Y chromosome in spermatocytes that may contribute to the activation of this heterochromatic chromosome.

    1. Chromosomes and Gene Expression
    2. Developmental Biology

    Transcription: A hub of activity

    Virginia L Pimmett, Mounia Lagha
    Insight

    Imaging experiments reveal the complex and dynamic nature of the transcriptional hubs associated with Notch signaling.