ArticleProceedings of the National Academy of Sciences of the United States of America2015
Functional organization of the human 4D Nucleome.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed, 121 citations in OpenAlex.
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- Transcriptional changes are tightly coupled to chromatin reorganization during cellular aging.Aging cell · 2024Article
- A unified approach of detecting phase transition in time-varying complex networks.Scientific reports · 2023Article
- Elucidating the structure and function of the nucleus-The NIH Common Fund 4D Nucleome program.Molecular cell · 2023Review
- Deciphering multi-way interactions in the human genome.Nature communications · 2022Article
- Rearrangement of T Cell genome architecture regulates GVHD.iScience · 2022Article
- Hodge theory-based biomolecular data analysis.Scientific reports · 2022Article
- Biomolecular Topology: Modelling and Analysis.Acta mathematica Sinica, English series · 2022Article
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- 4DNvestigator: time series genomic data analysis toolbox.Nucleus (Austin, Tex.) · 2021Article
- Valproic acid-induced changes of 4D nuclear morphology in astrocyte cells.Molecular biology of the cell · 2021Article
- Origins of human disease: the chrono-epigenetic perspective.Nature reviews. Genetics · 2021Review
- Tissue mechanics in stem cell fate, development, and cancer.Developmental cell · 2021Review
- Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars.BMC genomics · 2021Article
- The Circadian Clock and Viral Infections.Journal of biological rhythms · 2021Review
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- Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage.PLoS computational biology · 2020Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
Abstract
The 4D organization of the interphase nucleus, or the 4D Nucleome (4DN), reflects a dynamical interaction between 3D genome structure and function and its relationship to phenotype. We present initial analyses of the human 4DN, capturing genome-wide structure using chromosome conformation capture and 3D imaging, and function using RNA-sequencing. We introduce a quantitative index that measures underlying topological stability of a genomic region. Our results show that structural features of genomic regions correlate with function with surprising persistence over time. Furthermore, constructing genome-wide gene-level contact maps aided in identifying gene pairs with high potential for coregulation and colocalization in a manner consistent with expression via transcription factories. We additionally use 2D phase planes to visualize patterns in 4DN data. Finally, we evaluated gene pairs within a circadian gene module using 3D imaging, and found periodicity in the movement of clock circadian regulator and period circadian clock 2 relative to each other that followed a circadian rhythm and entrained with their expression.
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Registered trials
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