Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project
Dekker, Job ; Alber, Frank ; Aufmkolk, Sarah ; Beliveau, Brian J ; Bruneau, Benoit G ; Belmont, Andrew S ; Bintu, Lacramioara ; Boettiger, Alistair ; Calandrelli, Riccardo ; Disteche, Christine M ... show 10 more
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Authors
Alber, Frank
Aufmkolk, Sarah
Beliveau, Brian J
Bruneau, Benoit G
Belmont, Andrew S
Bintu, Lacramioara
Boettiger, Alistair
Calandrelli, Riccardo
Disteche, Christine M
Gilbert, David M
Gregor, Thomas
Hansen, Anders S
Huang, Bo
Huangfu, Danwei
Kalhor, Reza
Leslie, Christina S
Li, Wenbo
Li, Yun
Ma, Jian
Noble, William S
Park, Peter J
Phillips-Cremins, Jennifer E
Pollard, Katherine S
Rafelski, Susanne M
Ren, Bing
Ruan, Yijun
Shav-Tal, Yaron
Shen, Yin
Shendure, Jay
Shu, Xiaokun
Strambio-De-Castillia, Caterina
Vertii, Anastassiia
Zhang, Huaiying
Zhong, Sheng
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UMass Chan Affiliations
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Abstract
The four-dimensional nucleome (4DN) consortium studies the architecture of the genome and the nucleus in space and time. We summarize progress by the consortium and highlight the development of technologies for (1) mapping genome folding and identifying roles of nuclear components and bodies, proteins, and RNA, (2) characterizing nuclear organization with time or single-cell resolution, and (3) imaging of nuclear organization. With these tools, the consortium has provided over 2,000 public datasets. Integrative computational models based on these data are starting to reveal connections between genome structure and function. We then present a forward-looking perspective and outline current aims to (1) delineate dynamics of nuclear architecture at different timescales, from minutes to weeks as cells differentiate, in populations and in single cells, (2) characterize cis-determinants and trans-modulators of genome organization, (3) test functional consequences of changes in cis- and trans-regulators, and (4) develop predictive models of genome structure and function.
Source
Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Mol Cell. 2023 Aug 3;83(15):2624-2640. doi: 10.1016/j.molcel.2023.06.018. Epub 2023 Jul 6. PMID: 37419111; PMCID: PMC10528254.