Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function

被引:127
作者
McCord, Rachel Patton [1 ]
Kaplan, Noam [2 ]
Giorgetti, Luca [3 ]
机构
[1] Univ Tennessee, Dept Biochem & Cellular & Mol Biol, Knoxville, TN USA
[2] Technion Israel Inst Technol, Rappaport Fac Med, Dept Physiol Biophys & Syst Biol, Haifa, Israel
[3] Friedrich Miescher Inst Biomed Res, Basel, Switzerland
基金
欧洲研究理事会; 以色列科学基金会;
关键词
HI-C REVEALS; TOPOLOGICALLY ASSOCIATING DOMAINS; SCALE CHROMATIN ORGANIZATION; NUCLEAR LAMINA INTERACTIONS; SPATIAL-ORGANIZATION; GENOME ORGANIZATION; GENE-EXPRESSION; HIGH-RESOLUTION; X-CHROMOSOME; REGULATORY LANDSCAPES;
D O I
10.1016/j.molcel.2019.12.021
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
Rapidly developing technologies have recently fueled an exciting era of discovery in the field of chromosome structure and nuclear organization. In addition to chromosome conformation capture (3C) methods, new alternative techniques have emerged to study genome architecture and biological processes in the nucleus, often in single or living cells. This sets an unprecedented stage for exploring the mechanisms that link chromosome structure and biological function. Here we review popular as well as emerging approaches to study chromosome organization, focusing on the contribution of complementary methodologies to our understanding of structures revealed by 3C methods and their biological implications, and discuss the next technical and conceptual frontiers.
引用
收藏
页码:688 / 708
页数:21
相关论文
共 226 条
[51]   The second decade of 3C technologies: detailed insights into nuclear organization [J].
Denker, Annette ;
de laat, Wouter .
GENES & DEVELOPMENT, 2016, 30 (12) :1357-1382
[52]   Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture [J].
Despang, Alexandra ;
Schoepflin, Robert ;
Franke, Martin ;
Ali, Salaheddine ;
Jerkovic, Ivana ;
Paliou, Christina ;
Chan, Wing-Lee ;
Timmermann, Bernd ;
Wittler, Lars ;
Vingron, Martin ;
Mundlos, Stefan ;
Ibrahim, Daniel M. .
NATURE GENETICS, 2019, 51 (08) :1263-+
[53]   Transferable model for chromosome architecture [J].
Di Pierro, Michele ;
Zhang, Bin ;
Aiden, Erez Lieberman ;
Wolynes, Peter G. ;
Onuchic, Jose N. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2016, 113 (43) :12168-12173
[54]   A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo [J].
Diez-Roux, Graciana ;
Banfi, Sandro ;
Sultan, Marc ;
Geffers, Lars ;
Anand, Santosh ;
Rozado, David ;
Magen, Alon ;
Canidio, Elena ;
Pagani, Massimiliano ;
Peluso, Ivana ;
Lin-Marq, Nathalie ;
Koch, Muriel ;
Bilio, Marchesa ;
Cantiello, Immacolata ;
Verde, Roberta ;
De Masi, Cristian ;
Bianchi, Salvatore A. ;
Cicchini, Juliette ;
Perroud, Elodie ;
Mehmeti, Shprese ;
Dagand, Emilie ;
Schrinner, Sabine ;
Nuernberger, Asja ;
Schmidt, Katja ;
Metz, Katja ;
Zwingmann, Christina ;
Brieske, Norbert ;
Springer, Cindy ;
Hernandez, Ana Martinez ;
Herzog, Sarah ;
Grabbe, Frauke ;
Sieverding, Cornelia ;
Fischer, Barbara ;
Schrader, Kathrin ;
Brockmeyer, Maren ;
Dettmer, Sarah ;
Helbig, Christin ;
Alunni, Violaine ;
Battaini, Marie-Annick ;
Mura, Carole ;
Henrichsen, Charlotte N. ;
Garcia-Lopez, Raquel ;
Echevarria, Diego ;
Puelles, Eduardo ;
Garcia-Calero, Elena ;
Kruse, Stefan ;
Uhr, Markus ;
Kauck, Christine ;
Feng, Guangjie ;
Milyaev, Nestor .
PLOS BIOLOGY, 2011, 9 (01)
[55]   Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment [J].
Dileep, Vishnu ;
Wilson, Korey A. ;
Marchal, Claire ;
Lyu, Xiaowen ;
Zhao, Peiyao A. ;
Li, Ben ;
Poulet, Axel ;
Bartlett, Daniel A. ;
Rivera-Mulia, Juan Carlos ;
Qin, Zhaohui S. ;
Robins, Allan J. ;
Schulz, Thomas C. ;
Kulik, Michael J. ;
McCord, Rachel Patton ;
Dekker, Job ;
Dalton, Stephen ;
Corces, Victor G. ;
Gilbert, David M. .
STEM CELL REPORTS, 2019, 13 (01) :193-206
[56]   Topological domains in mammalian genomes identified by analysis of chromatin interactions [J].
Dixon, Jesse R. ;
Selvaraj, Siddarth ;
Yue, Feng ;
Kim, Audrey ;
Li, Yan ;
Shen, Yin ;
Hu, Ming ;
Liu, Jun S. ;
Ren, Bing .
NATURE, 2012, 485 (7398) :376-380
[57]   Dynamical network of residue-residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation [J].
Doshi, Urmi ;
Holliday, Michael J. ;
Eisenmesser, Elan Z. ;
Hamelberg, Donald .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2016, 113 (17) :4735-4740
[58]   A three-dimensional model of the yeast genome [J].
Duan, Zhijun ;
Andronescu, Mirela ;
Schutz, Kevin ;
McIlwain, Sean ;
Kim, Yoo Jung ;
Lee, Choli ;
Shendure, Jay ;
Fields, Stanley ;
Blau, C. Anthony ;
Noble, William S. .
NATURE, 2010, 465 (7296) :363-367
[59]   Tight protein-DNA interactions favor gene silencing [J].
Dubarry, Marion ;
Loiodice, Isabelle ;
Chen, Chunlong L. ;
Thermes, Claude ;
Taddei, Angela .
GENES & DEVELOPMENT, 2011, 25 (13) :1365-1370
[60]   Mutant lamins cause nuclear envelope rupture and DNA damage in skeletal muscle cells [J].
Earle, Ashley J. ;
Kirby, Tyler J. ;
Fedorchak, Gregory R. ;
Isermann, Philipp ;
Patel, Jineet ;
Iruvanti, Sushruta ;
Moore, Steven A. ;
Bonne, Gisele ;
Wallrath, Lori L. ;
Lammerding, Jan .
NATURE MATERIALS, 2020, 19 (04) :464-+