ArticleNature communications2021
Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer-promoter contact.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- A methodology to reduce the localization error in multi-loci microscopy provides new insights into enhancer biology.PLoS computational biology · 2025Article
- FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.ArXiv · 2025Article
- FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data.Nature methods · 2025Article
- ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization.PLoS computational biology · 2025Article
- AI analysis of super-resolution microscopy: Biological discovery in the absence of ground truth.The Journal of cell biology · 2024Review
- SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data.Communications biology · 2024Article
- SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data.bioRxiv : the preprint server for biology · 2024Article
- Image-based 3D genomics through chromatin tracing.Nature reviews. Methods primers · 2024Article
- ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization.bioRxiv : the preprint server for biology · 2023Article
- Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging.Nucleic acids research · 2023Article
- Revealing influencing factors on global waste distribution via deep-learning based dumpsite detection from satellite imagery.Nature communications · 2023Article
- Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila.Nature communications · 2022Article
- Article
- Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science.Entropy (Basel, Switzerland) · 2021Review
- Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies.Biophysical reports · 2021Review
Corrections and comments
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Authors and funding
4 authors.
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Abstract
Chromatin architecture plays an important role in gene regulation. Recent advances in super-resolution microscopy have made it possible to measure chromatin 3D structure and transcription in thousands of single cells. However, leveraging these complex data sets with a computationally unbiased method has been challenging. Here, we present a deep learning-based approach to better understand to what degree chromatin structure relates to transcriptional state of individual cells. Furthermore, we explore methods to "unpack the black box" to determine in an unbiased manner which structural features of chromatin regulation are most important for gene expression state. We apply this approach to an Optical Reconstruction of Chromatin Architecture dataset of the Bithorax gene cluster in Drosophila and show it outperforms previous contact-focused methods in predicting expression state from 3D structure. We find the structural information is distributed across the domain, overlapping and extending beyond domains identified by prior genetic analyses. Individual enhancer-promoter interactions are a minor contributor to predictions of activity.
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