ArticleGenome biology2023
A graph neural network-based interpretable framework reveals a novel DNA fragility-associated chromatin structural unit.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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.
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.
Who cites it
12 citing papers in PubMed, 18 citations in OpenAlex.
- Artificial Intelligence for Alzheimer's Disease Diagnosis: From Traditional Machine Learning to Large Language Models.Biosensors · 2026Review
- CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model.Genome biology · 2026Article
- AI-based methods for the assessment of DNA damage and repair mechanisms.Frontiers in systems biology · 2026Review
- From multi-omics to deep learning: advances in cfDNA-based liquid biopsy for multi-cancer screening.Biomarker research · 2025Review
- ChromInSight: Revealing DNA Double-Strand Breaks Through Chromatin Structural Insights With an Interpretable Graph Neural Network Framework.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- UV-induced reorganization of 3D genome mediates DNA damage response.Nature communications · 2025Article
- Towards the genomic sequence code of DNA fragility for machine learning.Nucleic acids research · 2024Article
- A spatial hierarchical network learning framework for drug repositioning allowing interpretation from macro to micro scale.Communications biology · 2024Article
- CGMega: explainable graph neural network framework with attention mechanisms for cancer gene module dissection.Nature communications · 2024Article
- Chromatin dynamics and RNA metabolism are double-edged swords for the maintenance of plant genome integrity.Nature plants · 2024Review
- Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair.Briefings in bioinformatics · 2024Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA double-strand breaks (DSBs) are among the most deleterious DNA lesions, and they can cause cancer if improperly repaired. Recent chromosome conformation capture techniques, such as Hi-C, have enabled the identification of relationships between the 3D chromatin structure and DSBs, but little is known about how to explain these relationships, especially from global contact maps, or their contributions to DSB formation.
resultsHere, we propose a framework that integrates graph neural network (GNN) to unravel the relationship between 3D chromatin structure and DSBs using an advanced interpretable technique GNNExplainer. We identify a new chromatin structural unit named the DNA fragility-associated chromatin interaction network (FaCIN). FaCIN is a bottleneck-like structure, and it helps to reveal a universal form of how the fragility of a piece of DNA might be affected by the whole genome through chromatin interactions. Moreover, we demonstrate that neck interactions in FaCIN can serve as chromatin structural determinants of DSB formation.
conclusionsOur study provides a more systematic and refined view enabling a better understanding of the mechanisms of DSB formation under the context of the 3D genome.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.