Evidence map›Paper›PMID 41187749›Full record

ArticleCell reports methods2025

Imaging the time course of DNA damage response at a nonrepetitive endogenous locus.

Adam T Rybczynski, W Taylor Cottle, Po-Ta Chen, Jiwoong Kwon, Tiantian Shang, Yanbo Wang, Paul Meneses, Sushil Pangeni, Yeji Park, Momcilo Gavrilov and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Adam T RybczynskiHoward Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
W Taylor CottleDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Po-Ta ChenHoward Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
Jiwoong KwonHoward Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
Tiantian ShangHoward Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
Yanbo WangDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Paul MenesesHoward Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Sushil PangeniHoward Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
Yeji ParkHoward Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
Momcilo GavrilovDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Taekjip HaHoward Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA. Electronic address: taekjip.ha@childrens.harvard.edu.

Funding

Single Molecule Studies of Nucleic Acids RemodelingR35GM122569 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Taekjip Ha · 2017 to 2026
$3.5M
Chromatin Function During Transcription and DNA Repair at Single Molecule Resolutionin Living CellsU01DK127432 · NIDDK · JOHNS HOPKINS UNIVERSITY · PI HA, TAEKJIP, JOHNSON, MARGARET ELLEN · 2020 to 2024
$3.5M
NIDDK NIH HHS U01 DK127432NIGMS NIH HHS R35 GM122569
6 · The paper itself

Abstract

DNA double-strand breaks (DSBs) are among the most genotoxic lesions. Investigating the cellular dynamics of repair factors during DSB repair requires methodologies that preserve both spatial and temporal information. Here, we describe a method for tracking repair progression over time at any desired genomic locus by combining DSB induction on the seconds timescale (very fast CRISPR) and genomic labeling using local genome denaturation (genome oligopaint via local denaturation fluorescence in situ hybridization [GOLDFISH]). Through protocol optimization to retain repair signatures such as γH2AX, p53-binding protein 1 (53BP1), and BRCA1, we show that the kinetics of DSB foci formation at nonrepetitive endogenous loci can be measured with minutes time resolution.

Indexed as

DNA DamageDNA RepairBRCA1 ProteinDNA Breaks, Double-StrandedHistonesHumansIn Situ Hybridization, FluorescenceTime FactorsTumor Suppressor p53-Binding Protein 1BRCA1 ProteinHistonesTumor Suppressor p53-Binding Protein 1CP: imagingCP: molecular biologyDNA damage responseDNA damage response kineticsDNA double-strand breaksDNA DSBDNA FISHDNA repairGOLDFISHvfCRISPR

Identifiers

PMID41187749
PMCPMC12664897

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.