D2 Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions
Abstract The execution of biological activities inside space‐limited cell nuclei requires sophisticated organization. Current studies on the 3D genome focus on chromatin interactions and local structures, e.g., topologically associating domains (TADs). In this study, two global physical properties:...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2022-10-01
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| Series: | Advanced Science |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/advs.202202149 |
| _version_ | 1797985725180805120 |
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| author | Yizhuo Che Xiaofei Yang Peng Jia Tingjie Wang Dan Xu Tianxue Guo Kai Ye |
| author_facet | Yizhuo Che Xiaofei Yang Peng Jia Tingjie Wang Dan Xu Tianxue Guo Kai Ye |
| author_sort | Yizhuo Che |
| collection | DOAJ |
| description | Abstract The execution of biological activities inside space‐limited cell nuclei requires sophisticated organization. Current studies on the 3D genome focus on chromatin interactions and local structures, e.g., topologically associating domains (TADs). In this study, two global physical properties: DNA density and distance to nuclear periphery (DisTP), are introduced and a 2D matrix, D2 plot, is constructed for mapping genetic and epigenetic markers. Distinct patterns of functional markers on the D2 plot, indicating its ability to compartmentalize functional genome regions, are observed. Furthermore, enrichments of transcription‐related markers are concatenated into a cross‐species transcriptional activation model, where the nucleus is divided into four areas: active, intermediate, repress and histone, and repress and repeat. Based on the trajectories of the genomic regions on D2 plot, the constantly active and newly activated genes are successfully identified during olfactory sensory neuron maturation. The analysis reveals that the D2 plot effectively categorizes functional regions and provides a universal and transcription‐related measurement for the 3D genome. |
| first_indexed | 2024-04-11T07:21:32Z |
| format | Article |
| id | doaj.art-e44c6c615efa4339b5d927730a965de3 |
| institution | Directory Open Access Journal |
| issn | 2198-3844 |
| language | English |
| last_indexed | 2024-04-11T07:21:32Z |
| publishDate | 2022-10-01 |
| publisher | Wiley |
| record_format | Article |
| series | Advanced Science |
| spelling | doaj.art-e44c6c615efa4339b5d927730a965de32022-12-22T04:37:11ZengWileyAdvanced Science2198-38442022-10-01930n/an/a10.1002/advs.202202149D2 Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome RegionsYizhuo Che0Xiaofei Yang1Peng Jia2Tingjie Wang3Dan Xu4Tianxue Guo5Kai Ye6School of Automation Science and Engineering Faculty of Electronic and Information Engineering Xi'an Jiaotong University Xi'an Shaanxi 710049 ChinaMOE Key Lab for Intelligent Networks and Networks Security Faculty of Electronic and Information Engineering Xi'an Jiaotong University Xi'an Shaanxi 710049 ChinaSchool of Automation Science and Engineering Faculty of Electronic and Information Engineering Xi'an Jiaotong University Xi'an Shaanxi 710049 ChinaSchool of Automation Science and Engineering Faculty of Electronic and Information Engineering Xi'an Jiaotong University Xi'an Shaanxi 710049 ChinaKey Laboratory of Biomedical Information Engineering of the Ministry of Education School of Life Sciences and Technology Xi'an Jiaotong University Xi'an Shaanxi 710049 ChinaSchool of Automation Science and Engineering Faculty of Electronic and Information Engineering Xi'an Jiaotong University Xi'an Shaanxi 710049 ChinaSchool of Automation Science and Engineering Faculty of Electronic and Information Engineering Xi'an Jiaotong University Xi'an Shaanxi 710049 ChinaAbstract The execution of biological activities inside space‐limited cell nuclei requires sophisticated organization. Current studies on the 3D genome focus on chromatin interactions and local structures, e.g., topologically associating domains (TADs). In this study, two global physical properties: DNA density and distance to nuclear periphery (DisTP), are introduced and a 2D matrix, D2 plot, is constructed for mapping genetic and epigenetic markers. Distinct patterns of functional markers on the D2 plot, indicating its ability to compartmentalize functional genome regions, are observed. Furthermore, enrichments of transcription‐related markers are concatenated into a cross‐species transcriptional activation model, where the nucleus is divided into four areas: active, intermediate, repress and histone, and repress and repeat. Based on the trajectories of the genomic regions on D2 plot, the constantly active and newly activated genes are successfully identified during olfactory sensory neuron maturation. The analysis reveals that the D2 plot effectively categorizes functional regions and provides a universal and transcription‐related measurement for the 3D genome.https://doi.org/10.1002/advs.2022021493D genomeDNA densitynuclear laminasingle‐cell Hi‐C |
| spellingShingle | Yizhuo Che Xiaofei Yang Peng Jia Tingjie Wang Dan Xu Tianxue Guo Kai Ye D2 Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions Advanced Science 3D genome DNA density nuclear lamina single‐cell Hi‐C |
| title | D2 Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions |
| title_full | D2 Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions |
| title_fullStr | D2 Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions |
| title_full_unstemmed | D2 Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions |
| title_short | D2 Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions |
| title_sort | d2 plot a matrix of dna density and distance to periphery reveals functional genome regions |
| topic | 3D genome DNA density nuclear lamina single‐cell Hi‐C |
| url | https://doi.org/10.1002/advs.202202149 |
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