Mapping the 3D genome architecture
The spatial organization of the genome plays a critical role in regulating gene expression, cellular differentiation, and genome stability. This review provides an in-depth examination of the methodologies, computational tools, and frameworks developed to map the three-dimensional (3D) architecture...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037024004392 |
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| author | Ghazaleh Tavallaee Elias Orouji |
| author_facet | Ghazaleh Tavallaee Elias Orouji |
| author_sort | Ghazaleh Tavallaee |
| collection | DOAJ |
| description | The spatial organization of the genome plays a critical role in regulating gene expression, cellular differentiation, and genome stability. This review provides an in-depth examination of the methodologies, computational tools, and frameworks developed to map the three-dimensional (3D) architecture of the genome, focusing on both ligation-based and ligation-free techniques. We also explore the limitations of these methods, including biases introduced by restriction enzyme digestion and ligation inefficiencies, and compare them to more recent ligation-free approaches such as Genome Architecture Mapping (GAM) and Split-Pool Recognition of Interactions by Tag Extension (SPRITE). These techniques offer unique insights into higher-order chromatin structures by bypassing ligation steps, thus enabling the capture of complex multi-way interactions that are often challenging to resolve with traditional methods. Furthermore, we discuss the integration of chromatin interaction data with other genomic layers through multimodal approaches, including recent advances in single-cell technologies like sci-HiC and scSPRITE, which help unravel the heterogeneity of chromatin architecture in development and disease. |
| format | Article |
| id | doaj-art-2ad5de6d8c464818a3bf48592dffa64f |
| institution | DOAJ |
| issn | 2001-0370 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj-art-2ad5de6d8c464818a3bf48592dffa64f2025-08-20T02:51:11ZengElsevierComputational and Structural Biotechnology Journal2001-03702025-01-01278910110.1016/j.csbj.2024.12.018Mapping the 3D genome architectureGhazaleh Tavallaee0Elias Orouji1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, CanadaCorrespondence to: Epigenomics Lab, Princess Margaret Cancer Centre, University Health Network (UHN), 101 College St., Toronto, ON M5G 1L7, Canada.; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, CanadaThe spatial organization of the genome plays a critical role in regulating gene expression, cellular differentiation, and genome stability. This review provides an in-depth examination of the methodologies, computational tools, and frameworks developed to map the three-dimensional (3D) architecture of the genome, focusing on both ligation-based and ligation-free techniques. We also explore the limitations of these methods, including biases introduced by restriction enzyme digestion and ligation inefficiencies, and compare them to more recent ligation-free approaches such as Genome Architecture Mapping (GAM) and Split-Pool Recognition of Interactions by Tag Extension (SPRITE). These techniques offer unique insights into higher-order chromatin structures by bypassing ligation steps, thus enabling the capture of complex multi-way interactions that are often challenging to resolve with traditional methods. Furthermore, we discuss the integration of chromatin interaction data with other genomic layers through multimodal approaches, including recent advances in single-cell technologies like sci-HiC and scSPRITE, which help unravel the heterogeneity of chromatin architecture in development and disease.http://www.sciencedirect.com/science/article/pii/S20010370240043923D genome architectureChromatin conformation captureHi-CSingle-cell genomicsEpigenomicsChromatin |
| spellingShingle | Ghazaleh Tavallaee Elias Orouji Mapping the 3D genome architecture Computational and Structural Biotechnology Journal 3D genome architecture Chromatin conformation capture Hi-C Single-cell genomics Epigenomics Chromatin |
| title | Mapping the 3D genome architecture |
| title_full | Mapping the 3D genome architecture |
| title_fullStr | Mapping the 3D genome architecture |
| title_full_unstemmed | Mapping the 3D genome architecture |
| title_short | Mapping the 3D genome architecture |
| title_sort | mapping the 3d genome architecture |
| topic | 3D genome architecture Chromatin conformation capture Hi-C Single-cell genomics Epigenomics Chromatin |
| url | http://www.sciencedirect.com/science/article/pii/S2001037024004392 |
| work_keys_str_mv | AT ghazalehtavallaee mappingthe3dgenomearchitecture AT eliasorouji mappingthe3dgenomearchitecture |