ArticleNature methods2025
Perturb-tracing enables high-content screening of multi-scale 3D genome regulators.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Fast, StreamlinedChemical & biomedical imaging · 2026Article
- Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT.Nature biotechnology · 2026Article
- A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Whole-genome 3D architectural screen reveals modulators of brain DNA structure.bioRxiv : the preprint server for biology · 2026Article
- RB loss modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions.Nature communications · 2026Article
- Differential analysis of image-based chromatin tracing data with Dory.bioRxiv : the preprint server for biology · 2026Article
- Article
- FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.ArXiv · 2025Article
- The DNA Repair Component EEPD1 Regulates Actin Polymerization.Biology of the cell · 2025Article
- Regulation of epigenetics and chromosome structure by human ORC2.Cell reports · 2025Article
- 3D Genome Engineering: Current Advances and Therapeutic Opportunities in Human Diseases.Research (Washington, D.C.) · 2025Review
- Chromosome compartmentalization: causes, changes, consequences, and conundrums.Trends in cell biology · 2024Review
- Review
- Image-based 3D genomics through chromatin tracing.Nature reviews. Methods primers · 2024Article
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12 authors.
Funding
Abstract
Three-dimensional (3D) genome organization becomes altered during development, aging and disease, but the factors regulating chromatin topology are incompletely understood and currently no technology can efficiently screen for new regulators of multi-scale chromatin organization. Here, we developed an image-based high-content screening platform (Perturb-tracing) that combines pooled CRISPR screens, a cellular barcode readout method (BARC-FISH) and chromatin tracing. We performed a loss-of-function screen in human cells, and visualized alterations to their 3D chromatin folding conformations, alongside perturbation-paired barcode readout in the same single cells. We discovered tens of new regulators of chromatin folding at different length scales, ranging from chromatin domains and compartments to chromosome territory. A subset of the regulators exhibited 3D genome effects associated with loop extrusion and A-B compartmentalization mechanisms, while others were largely unrelated to these known 3D genome mechanisms. Finally, we identified new regulators of nuclear architectures and found a functional link between chromatin compaction and nuclear shape. Altogether, our method enables scalable, high-content identification of chromatin and nuclear topology regulators that will stimulate new insights into the 3D genome.
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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.