Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project
Job Dekker
(1, 2)
,
Frank Alber
(3)
,
Sarah Aufmkolk
(4)
,
Brian J Beliveau
(5)
,
Benoit G Bruneau
(6, 7)
,
Andrew S Belmont
(8)
,
Lacramioara Bintu
(9)
,
Alistair Boettiger
(9)
,
Riccardo Calandrelli
(10)
,
Christine M Disteche
(5)
,
David M Gilbert
(11)
,
Thomas Gregor
(12)
,
Anders S Hansen
(13)
,
Bo Huang
(7)
,
Danwei Huangfu
(14)
,
Reza Kalhor
(15)
,
Christina S Leslie
(14)
,
Wenbo Li
(16)
,
Yun Li
(17)
,
Jian Ma
(18)
,
William S Noble
(5)
,
Peter J Park
(4)
,
Jennifer E Phillips-Cremins
(19)
,
Katherine S Pollard
(6, 7, 20)
,
Susanne M Rafelski
(21)
,
Bing Ren
(10)
,
Yijun Ruan
(22)
,
Yaron Shav-Tal
(23)
,
Yin Shen
(7)
,
Jay Shendure
(5)
,
Xiaokun Shu
(7)
,
Caterina Strambio-De-Castillia
(1)
,
Anastassiia Vertii
(1)
,
Huaiying Zhang
(18)
,
Sheng Zhong
(10)
1
UMass Boston -
University of Massachusetts [Boston]
2 HHMI - Howard Hughes Medical Institute [Chevy Chase]
3 UCLA - University of California [Los Angeles]
4 HMS - Harvard Medical School [Boston]
5 University of Washington [Seattle]
6 Gladstone Institutes [San Francisco]
7 UC San Francisco - University of California [San Francisco]
8 UIUC - University of Illinois at Urbana-Champaign [Urbana]
9 Stanford University
10 UC San Diego - University of California [San Diego]
11 SDBRI - San Diego Biomedical Research Institute
12 Princeton University
13 MIT - Massachusetts Institute of Technology
14 MSKCC - Memorial Sloan Kettering Cancer Center
15 JHU - Johns Hopkins University
16 UTHealth - The University of Texas Health Science Center at Houston
17 UNC - University of North Carolina [Chapel Hill]
18 CMU - Carnegie Mellon University [Pittsburgh]
19 University of Pennsylvania
20 Chan Zuckerberg BioHub [San Francisco, CA]
21 Allen Institute [Seattle]
22 Zhejiang University [Hangzhou, China]
23 Bar-Ilan University [Israël]
2 HHMI - Howard Hughes Medical Institute [Chevy Chase]
3 UCLA - University of California [Los Angeles]
4 HMS - Harvard Medical School [Boston]
5 University of Washington [Seattle]
6 Gladstone Institutes [San Francisco]
7 UC San Francisco - University of California [San Francisco]
8 UIUC - University of Illinois at Urbana-Champaign [Urbana]
9 Stanford University
10 UC San Diego - University of California [San Diego]
11 SDBRI - San Diego Biomedical Research Institute
12 Princeton University
13 MIT - Massachusetts Institute of Technology
14 MSKCC - Memorial Sloan Kettering Cancer Center
15 JHU - Johns Hopkins University
16 UTHealth - The University of Texas Health Science Center at Houston
17 UNC - University of North Carolina [Chapel Hill]
18 CMU - Carnegie Mellon University [Pittsburgh]
19 University of Pennsylvania
20 Chan Zuckerberg BioHub [San Francisco, CA]
21 Allen Institute [Seattle]
22 Zhejiang University [Hangzhou, China]
23 Bar-Ilan University [Israël]
Thomas Gregor
- Fonction : Auteur
- PersonId : 745828
- IdHAL : tgregor
- ORCID : 0000-0001-9460-139X
- IdRef : 189979542
Sheng Zhong
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- Fonction : Auteur correspondant
- PersonId : 1278465
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Résumé
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 cisand trans-regulators, and (4) develop predictive models of genome structure and function.