Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution
Abstract The dynamic three-dimensional spatial conformations of chromosomes demonstrate complex structural variations across single cells, which plays pivotal roles in modulating single-cell specific transcription and epigenetics landscapes. The high rates of missing contacts in single-cell chromati...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-04-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-58674-w |
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| author | Hao Wang Jiaxin Yang Xinrui Yu Yu Zhang Jianliang Qian Jianrong Wang |
| author_facet | Hao Wang Jiaxin Yang Xinrui Yu Yu Zhang Jianliang Qian Jianrong Wang |
| author_sort | Hao Wang |
| collection | DOAJ |
| description | Abstract The dynamic three-dimensional spatial conformations of chromosomes demonstrate complex structural variations across single cells, which plays pivotal roles in modulating single-cell specific transcription and epigenetics landscapes. The high rates of missing contacts in single-cell chromatin contact maps impose significant challenges to reconstruct high-resolution spatial chromatin configurations. We develop a data-driven algorithm, Tensor-FLAMINGO, based on a low-rank tensor completion strategy. Implemented on a diverse panel of single-cell chromatin datasets, Tensor-FLAMINGO generates 10kb- and 30kb-resolution spatial chromosomal architectures across individual cells. Tensor-FLAMINGO achieves superior accuracy in reconstructing 3D chromatin structures, recovering missing contacts, and delineating cell clusters. The unprecedented high-resolution characterization of single-cell genome folding enables expanded identification of single-cell specific long-range chromatin interactions, multi-way spatial hubs, and the mechanisms of disease-associated GWAS variants. Beyond the sparse 2D contact maps, the complete 3D chromatin conformations promote an avenue to understand the dynamics of spatially coordinated molecular processes across different cells. |
| format | Article |
| id | doaj-art-5e5edc0b4f744b5193b4bf934c1d66f9 |
| institution | OA Journals |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-5e5edc0b4f744b5193b4bf934c1d66f92025-08-20T02:17:13ZengNature PortfolioNature Communications2041-17232025-04-0116112210.1038/s41467-025-58674-wTensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolutionHao Wang0Jiaxin Yang1Xinrui Yu2Yu Zhang3Jianliang Qian4Jianrong Wang5Department of Computational Mathematics, Science and Engineering, Michigan State UniversityDepartment of Computational Mathematics, Science and Engineering, Michigan State UniversityDepartment of Computational Mathematics, Science and Engineering, Michigan State UniversityDepartment of Microbiology, Genetics, and Immunology, Michigan State UniversityDepartment of Computational Mathematics, Science and Engineering, Michigan State UniversityDepartment of Computational Mathematics, Science and Engineering, Michigan State UniversityAbstract The dynamic three-dimensional spatial conformations of chromosomes demonstrate complex structural variations across single cells, which plays pivotal roles in modulating single-cell specific transcription and epigenetics landscapes. The high rates of missing contacts in single-cell chromatin contact maps impose significant challenges to reconstruct high-resolution spatial chromatin configurations. We develop a data-driven algorithm, Tensor-FLAMINGO, based on a low-rank tensor completion strategy. Implemented on a diverse panel of single-cell chromatin datasets, Tensor-FLAMINGO generates 10kb- and 30kb-resolution spatial chromosomal architectures across individual cells. Tensor-FLAMINGO achieves superior accuracy in reconstructing 3D chromatin structures, recovering missing contacts, and delineating cell clusters. The unprecedented high-resolution characterization of single-cell genome folding enables expanded identification of single-cell specific long-range chromatin interactions, multi-way spatial hubs, and the mechanisms of disease-associated GWAS variants. Beyond the sparse 2D contact maps, the complete 3D chromatin conformations promote an avenue to understand the dynamics of spatially coordinated molecular processes across different cells.https://doi.org/10.1038/s41467-025-58674-w |
| spellingShingle | Hao Wang Jiaxin Yang Xinrui Yu Yu Zhang Jianliang Qian Jianrong Wang Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution Nature Communications |
| title | Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution |
| title_full | Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution |
| title_fullStr | Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution |
| title_full_unstemmed | Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution |
| title_short | Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution |
| title_sort | tensor flamingo unravels the complexity of single cell spatial architectures of genomes at high resolution |
| url | https://doi.org/10.1038/s41467-025-58674-w |
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