Genome-wide profiling of DNA repair proteins in single cells
Accurate repair of DNA damage is critical for maintenance of genomic integrity and cellular viability. Because damage occurs non-uniformly across the genome, single-cell resolution is required for proper interrogation, but sensitive detection has remained challenging. Here, we present a comprehensive analysis of repair protein localization in single human cells using DamID and ChIC sequencing techniques. This study reports genome-wide binding profiles in response to DNA double-strand breaks induced by AsiSI, and explores variability in genomic damage locations and associated repair features in the context of spatial genome organization. By unbiasedly detecting repair factor localization, we find that repair proteins often occupy entire topologically associating domains, mimicking variability in chromatin loop anchoring. Moreover, we demonstrate the formation of multi-way chromatin hubs in response to DNA damage. Notably, larger hubs show increased coordination of repair protein binding, suggesting a preference for cooperative repair mechanisms. Together, our work offers insights into the heterogeneous processes underlying genome stability in single cells.
Authors
- Jop Kind (ORCID: https://orcid.org/0000-0001-7538-2638)
- Joanna W. Jachowicz (ORCID: https://orcid.org/0000-0002-1599-682X)
- Magdalena A. Karpińska (ORCID: https://orcid.org/0000-0002-1516-2083)
- A. Marieke Oudelaar (ORCID: https://orcid.org/0000-0002-4016-6158)
- Lőrinc Sándor Pongor (ORCID: https://orcid.org/0000-0001-5917-4628)
- Pim M. J. Rullens (ORCID: https://orcid.org/0009-0007-4176-5674)
- Kim L. de Luca (ORCID: https://orcid.org/0000-0002-5900-5100)
- Sandra S. de Vries (ORCID: https://orcid.org/0000-0002-7477-2447)
- Gaëlle Legube (ORCID: https://orcid.org/0000-0002-4784-2702)
- Agnieszka Gacek‐Matthews (ORCID: https://orcid.org/0000-0001-5884-583X)
Institutions
- Institute of Molecular Biotechnology (AT)
- Centre National de la Recherche Scientifique (FR)
- Royal Netherlands Academy of Arts and Sciences (NL)
- Austrian Academy of Sciences (AT)
- Radboud University Nijmegen (NL)
- Université Fédérale de Toulouse Midi-Pyrénées (FR)
- Radboud University Medical Center (NL)
- University Medical Center Utrecht (NL)
- Radboud Institute for Molecular Life Sciences (NL)
- Oncode Institute (NL)
- Hubrecht Institute for Developmental Biology and Stem Cell Research (NL)
- Vienna Biocenter (AT)
- Max Planck Institute for Multidisciplinary Sciences (DE)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-11-21
- DOI
- https://doi.org/10.1038/s41467-024-54159-4
- Citations
- 12
- Primary Topic
- DNA Repair Mechanisms
- Type
- article
- Field-Weighted Citation Impact
- 2.81
Funders
- US-UK Fulbright Commission
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek
- Max-Planck-Gesellschaft
- Oncode Institute