Spatial and temporal organization of the genome Current state and future aims of the 4D nucleome project

被引：14

作者：

Dekker, Job ^{[1
,2
]}

Alber, Frank ^{[3
]}

Aufmkolk, Sarah ^{[4
]}

Beliveau, Brian J. ^{[5
]}

Bruneau, Benoit G. ^{[6
]}

Belmont, Andrew S. ^{[7
]}

Bintu, Lacramioara ^{[8
]}

Boettiger, Alistair ^{[8
]}

Calandrelli, Riccardo ^{[9
]}

Disteche, Christine M. ^{[5
]}

Gilbert, David M. ^{[22
]}

Gregor, Thomas ^{[10
]}

Hansen, Anders S. ^{[11
]}

Huang, Bo ^{[12
]}

Huangfu, Danwei ^{[13
]}

Kalhor, Reza ^{[14
]}

Leslie, Christina S. ^{[13
]}

Li, Wenbo ^{[15
]}

Li, Yun ^{[16
]}

Ma, Jian ^{[17
]}

Noble, William S. ^{[5
]}

Park, Peter J. ^{[4
]}

Phillips-Cremins, Jennifer E. ^{[18
]}

Pollard, Katherine S. ^{[6
,12
,23
]}

Rafelski, Susanne M. ^{[19
]}

Ren, Bing ^{[9
]}

Ruan, Yijun ^{[20
]}

Shav-Tal, Yaron ^{[21
]}

Shen, Yin ^{[12
]}

Shendure, Jay ^{[5
]}

Shu, Xiaokun ^{[12
]}

Strambio-De-Castillia, Caterina ^{[1
]}

Vertii, Anastassiia ^{[1
]}

Zhang, Huaiying ^{[17
]}

Zhong, Sheng ^{[9
]}

机构：

[1] Univ Massachusetts, Chan Med Sch, Boston, MA 02215 USA

[2] Howard Hughes Med Inst, Chevy Chase, MD 20815 USA

[3] Univ Calif Los Angeles, Los Angeles, CA USA

[4] Harvard Med Sch, Boston, MA USA

[5] Univ Washington, Seattle, WA USA

[6] Gladstone Inst, San Francisco, CA USA

[7] Univ Illinois, Urbana, IL USA

[8] Stanford Univ, Stanford, CA USA

[9] Univ Calif San Diego, La Jolla, CA 92093 USA

[10] Princeton Univ, Princeton, NJ USA

[11] MIT, Cambridge, MA USA

[12] Univ Calif San Francisco, San Francisco, CA USA

[13] Mem Sloan Kettering Canc Ctr, New York, NY USA

[14] Johns Hopkins Univ, Baltimore, MD USA

[15] Univ Texas Hlth Sci Ctr Houston, Houston, TX USA

[16] Univ N Carolina, Gillings Sch Global Publ Hlth, Chapel Hill, NC USA

[17] Carnegie Mellon Univ, Pittsburgh, PA USA

[18] Univ Penn, Philadelphia, PA USA

[19] Allen Inst, Seattle, WA USA

[20] Zhejiang Univ, Hangzhou, Zhejiang, Peoples R China

[21] Bar Ilan Univ, Ramat Gan, Israel

[22] San Diego Biomed Res Inst, San Diego, CA USA

[23] Chan Zuckerberg Biohub, San Francisco, CA USA

来源：

MOLECULAR CELL | 2023年 / 83卷 / 15期

关键词：

IN-SITU HYBRIDIZATION; PHASE-SEPARATION; 3D GENOME; DNA LOCI; CHROMATIN; SCALE; PROBES; FISH; VISUALIZATION; SEQUENCES;

D O I：

10.1016/j.molcel.2023.06.018

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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) char-acterize 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.

引用

页码：2624 / 2640

页数：17

共 50 条

[1] The 4D nucleome project
Dekker, Job
Belmont, Andrew S.
Guttman, Mitchell
Leshyk, Victor O.
Lis, John T.
Lomvardas, Stavros
Mirny, Leonid A.
O'Shea, Clodagh C.
Park, Peter J.
Ren, Bing
Politz, Joan C. Ritland
Shendure, Jay
Zhong, Sheng
van den Berg, Aafke
Heckert, Alec Basil
Bertero, Alessandro
Bortnick, Alex
Kukalev, Alexander
Moore, Amanda
Pombo, Ana
Hansen, Anders Sejr
Chiariello, Andrea Maria
Sali, Andrej
Belmont, Andrew
Stephens, Andrew
Nand, Ankita
Valton, Anne-Laure
Goloborodko, Anton
He, Arthur
van Steensel, Bas
Webb, Ben
Roscoe, Benjamin
Li, Bin
Ren, Bing
Chait, Brian
Blau, C. Anthony
Annunziatella, Carlo
Ware, Carol
Wei, Chia Lin
Leemans, Christ
Disteche, Christine
Jarjour, Christine
Thieme, Christoph
Murry, Chuck
Barcia, Claudia Trevilla
Trapnell, Cole
Murre, Cornelis
Peric-Hupkes, Daan
Simon, Dan
Bartlett, Daniel
[J]. NATURE, 2017, 549 (7671) : 219 - 226
[2] The 4D nucleome project
Job Dekker
Andrew S. Belmont
Mitchell Guttman
Victor O. Leshyk
John T. Lis
Stavros Lomvardas
Leonid A. Mirny
Clodagh C. O’Shea
Peter J. Park
Bing Ren
Joan C. Ritland Politz
Jay Shendure
Sheng Zhong
[J]. Nature, 2017, 549 : 219 - 226
[3] The 3D organization of genome in the nucleus: from the nucleosome to the 4D nucleome
Guohong Li
[J]. Science China Life Sciences, 2020, 63 : 791 - 794
[4] Functional organization of the human 4D Nucleome
Chen, Haiming
Chen, Jie
Muir, Lindsey A.
Ronquist, Scott
Meixner, Walter
Ljungman, Mats
Ried, Thomas
Smale, Stephen
Rajapakse, Indika
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2015, 112 (26) : 8002 - 8007
[5] The 3D organization of genome in the nucleus: from the nucleosome to the 4D nucleome
Guohong Li
[J]. Science China(Life Sciences)., 2020, 63 (06) - 794
[6] The 3D organization of genome in the nucleus: from the nucleosome to the 4D nucleome
Guohong Li
[J]. Science China Life Sciences, 2020, (06) : 791 - 794
[7] Correction: Corrigendum: The 4D nucleome project
Job Dekker
Andrew S. Belmont
Mitchell Guttman
Victor O. Leshyk
John T. Lis
Stavros Lomvardas
Leonid A. Mirny
Clodagh C. O’Shea
Peter J. Park
Bing Ren
Joan C. Ritland Politz
Jay Shendure
Sheng Zhong
[J]. Nature, 2017, 552 (7684) : 278 - 278
[8] The 3D organization of genome in the nucleus: from the nucleosome to the 4D nucleome
Li, Guohong
[J]. SCIENCE CHINA-LIFE SCIENCES, 2020, 63 (06) : 791 - 794
[9] 4D nucleome: dynamic three-dimensional genome organization over time
Kim, Hyoung-Pyo
[J]. EXPERIMENTAL AND MOLECULAR MEDICINE, 2024, 56 (04): : 761 - 762
[10] The 4D Nucleome: Genome Compartmentalization in an Evolutionary Context
T. Cremer
M. Cremer
C. Cremer
[J]. Biochemistry (Moscow), 2018, 83 : 313 - 325

← 1 2 3 4 5 →