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The 4D nucleome project
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Abstract
The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights into how the nucleus is organized and functions. The project will develop and benchmark experimental and computational approaches for measuring genome conformation and nuclear organization, and investigate how these contribute to gene regulation and other genome functions. Validated experimental technologies will be combined with biophysical approaches to generate quantitative models of spatial genome organization in different biological states, both in cell populations and in single cells.
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““4D mapping” of chromatin interactions (i.e., brain regions across developmental time) is critical for understanding the functional relationships of regulatory regions to genes (Dekker et al., 2017)”
From Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders (2019) · cites this paper as Dekker et al., 2017
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Additional file 1 of Inferring chromosome radial organization from Hi-C data
Das, P., Shen, T., & McCord, R. P. (2020) · Figshare · doi:10.6084/m9.figshare.13211987
Liu, N., Sadlon, T. J., Wong, Y. Y., Pederson, S., Breen, J., & Barry, S. C. (2022) · Figshare · doi:10.6084/m9.figshare.20206400
Miko, H., Qiu, Y., Gaertner, B., Sander, M., & Ohler, U. (2021) · Figshare · doi:10.6084/m9.figshare.13662654
Miko, H., Qiu, Y., Gaertner, B., Sander, M., & Ohler, U. (2021) · Figshare · doi:10.6084/m9.figshare.13662624
Ardakany, A. R., Gezer, H. T., Lonardi, S., & Ay, F. (2020) · Figshare · doi:10.6084/m9.figshare.13031597
Shah, P. P., Keough, K. C., Gjoni, K., Santini, G. T., Abdill, R. J., Wickramasinghe, N. M., Dundes, C. E., Karnay, A. M., Chen, A. C., Salomon, R. E. A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26563459
Pujadas-Liwag, E. M., Wei, X., Acosta, N., Carter, L. M., Yang, J., Almassalha, L. M., Jain, S., Daneshkhah, A., Rao, S. S. P., Seker-Polat, F., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26696598
Kai, Y., Liu, N., Orkin, S. H., & Yuan, G. (2024) · Figshare · doi:10.6084/m9.figshare.26626546
Shah, P. P., Keough, K. C., Gjoni, K., Santini, G. T., Abdill, R. J., Wickramasinghe, N. M., Dundes, C. E., Karnay, A. M., Chen, A. C., Salomon, R. E. A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26563462
Kai, Y., Liu, N., Orkin, S. H., & Yuan, G. (2023) · Figshare · doi:10.6084/m9.figshare.24309953
Miko, H., Qiu, Y., Gaertner, B., Sander, M., & Ohler, U. (2021) · Figshare · doi:10.6084/m9.figshare.13662642
Deng, L., Gao, B., Zhao, L., Zhang, Y., Zhang, Q., Guo, M., Yang, Y., Wang, S., Xie, L., Lou, H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.17982467
Additional file 6 of SPIN reveals genome-wide landscape of nuclear compartmentalization
Wang, Y., Zhang, Y., Zhang, R., van Schaik, T., Zhang, L., Sasaki, T., Peric‐Hupkes, D., Chen, Y., Gilbert, D. M., van Steensel, B., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13579170
Self-citationShah, P. P., Keough, K. C., Gjoni, K., Santini, G. T., Abdill, R. J., Wickramasinghe, N. M., Dundes, C. E., Karnay, A. M., Chen, A. C., Salomon, R. E. A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26563456
Miko, H., Qiu, Y., Gaertner, B., Sander, M., & Ohler, U. (2021) · Figshare · doi:10.6084/m9.figshare.13662648
Pujadas-Liwag, E. M., Wei, X., Acosta, N., Carter, L. M., Yang, J., Almassalha, L. M., Jain, S., Daneshkhah, A., Rao, S. S. P., Seker-Polat, F., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26696601
Additional file 2 of Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D
Zheng, Y., Shen, S., & Keleş, S. (2022) · Figshare · doi:10.6084/m9.figshare.21351410
Additional file 2 of Epiphany: predicting Hi-C contact maps from 1D epigenomic signals
Yang, R., Das, A., Gao, V. R., Karbalayghareh, A., Noble, W. S., Bilmes, J. A., & Leslie, C. S. (2024) · Figshare · doi:10.6084/m9.figshare.26594546
Additional file 4 of Epiphany: predicting Hi-C contact maps from 1D epigenomic signals
Yang, R., Das, A., Gao, V. R., Karbalayghareh, A., Noble, W. S., Bilmes, J. A., & Leslie, C. S. (2024) · Figshare · doi:10.6084/m9.figshare.26594552
Additional file 2 of SPIN reveals genome-wide landscape of nuclear compartmentalization
Wang, Y., Zhang, Y., Zhang, R., van Schaik, T., Zhang, L., Sasaki, T., Peric‐Hupkes, D., Chen, Y., Gilbert, D. M., van Steensel, B., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13579158
Self-citationWeng, Z., Ruan, F., Chen, W., Chen, Z., Xie, Y., Luo, M., Xie, Z., Zhang, C., Wang, J., Sun, Y., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623496
Additional file 1 of Epiphany: predicting Hi-C contact maps from 1D epigenomic signals
Yang, R., Das, A., Gao, V. R., Karbalayghareh, A., Noble, W. S., Bilmes, J. A., & Leslie, C. S. (2024) · Figshare · doi:10.6084/m9.figshare.26594540
Miko, H., Qiu, Y., Gaertner, B., Sander, M., & Ohler, U. (2021) · Figshare · doi:10.6084/m9.figshare.13662627
Kruse, K., Hug, C. B., & Vaquerizas, J. M. (2020) · Figshare · doi:10.6084/m9.figshare.13467409
Metadata
- Authors
- the 4D Nucleome Network, Dekker, J., Belmont, A. S., Guttman, M., Leshyk, V. O., Lis, J. T., Lomvardas, S., Mirny, L. A., O’Shea, C. C., Park, P. J., Ren, B., Politz, J. C. R., Shendure, J., & Zhong, S.
- Affiliations
- Howard Hughes Medical Institute (US)
- California Institute of Technology (US)
- Cornell University (US)
- Mortimer B. Zuckerman Mind Brain Behavior Institute (US)
- Salk Institute for Biological Studies (US)
- Harvard University (US)
- University of California San Diego (US)
- Corresponding author
- Dekker, Job
- ORCID
- Venue
- Nature
- Published
- 2017-09-14
- Volume
- 549
- Issue
- 7671
- Pages
- 219-226
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC5617335
- OpenAlex
- W2584394140
- Cited by
- 732
- References
- 118
- Citations by year
- 2026: 63 · 2025: 74 · 2024: 81 · 2023: 74 · 2022: 96 · 2021: 110 · 2020: 82 · 2019: 73 · 2018: 65 · 2017: 13
- FWCI
- 26.04
- Type
- journal article
- Language
- en
- Update notices
- erratum (2017-11-22)
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship@UMassChan (submittedVersion, cc-by-nc-nd)
- UWA Profiles and Research Repository (UWA) (submittedVersion)
- ReIn UW (University of Warsaw) (submittedVersion, cc-by-nc-nd)
- Funders
- National Institutes of Health
- National Heart, Lung, and Blood Institute (U01HL129998, U01HL129958)
- National Institute on Drug Abuse (U01DA040582)
- NIH Office of the Director
- National Cancer Institute (U01CA200060)
- National Institute on Deafness and Other Communication Disorders (R01DC013560)
- National Institute of General Medical Sciences (P50GM085764)
- National Institute of Diabetes and Digestive and Kidney Diseases (U54DK107977, U54DK107965, U54DK107980, U54DK107979)
- National Institute of Biomedical Imaging and Bioengineering (U01EB021223)
- Common Fund (1U01DA040709)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- 3D genome organization, nuclear organization, gene expression regulation, single-cell genomics, human genome, mouse genome, chromatin dynamics
- MeSH terms
- Animals, Cell Line, Cell Nucleus, Chromatin, Chromosomes, Goals, Humans, Models, Biological, Models, Molecular, Reproducibility of Results, Genome, Genomics, Information Dissemination, Mice, Molecular Imaging, Single-Cell Analysis, Spatio-Temporal Analysis
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