Rapid reversible changes in compartments and local chromatin organization revealed by hyperosmotic shock

被引:35
作者
Amat, Ramon [1 ,2 ]
Bottcher, Rene [1 ,2 ]
Le Dily, Francois [3 ]
Vidal, Enrique [3 ]
Quilez, Javier [3 ]
Cuartero, Yasmina [3 ,4 ]
Beato, Miguel [3 ,4 ,5 ]
de Nadal, Eulalia [1 ,2 ]
Posas, Francesc [1 ,2 ]
机构
[1] Univ Pompeu Fabra, Dept Ciencies Expt & Salut, Cell Signaling Res Grp, E-08003 Barcelona, Spain
[2] Barcelona Inst Sci & Technol, Inst Res Biomed IRB Barcelona, Barcelona 08028, Spain
[3] Ctr Genom Regulat CRG, Gene Regulat Stem Cells & Canc Program, E-08003 Barcelona, Spain
[4] Barcelona Inst Sci & Technol BIST, CNAG CRG, E-08003 Barcelona, Spain
[5] Univ Pompeu Fabra, Barcelona 08003, Spain
基金
欧洲研究理事会;
关键词
TOPOLOGICALLY ASSOCIATING DOMAINS; PHASE-SEPARATION; MAMMALIAN GENOMES; 3D GENOME; TRANSCRIPTION; COHESIN; PRINCIPLES; CTCF; CONDENSATION; ACTIVATION;
D O I
10.1101/gr.238527.118
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
Nuclear architecture is decisive for the assembly of transcriptional responses. However, how chromosome organization is dynamically modulated to permit rapid and transient transcriptional changes in response to environmental challenges remains unclear. Here we show that hyperosmotic stress disrupts different levels of chromosome organization, ranging from A/B compartment changes to reduction in the number and insulation of topologically associating domains (TADs). Concomitantly, transcription is greatly affected, TAD borders weaken, and RNA Polymerase II runs off from hundreds of transcription end sites. Stress alters the binding profiles of architectural proteins, which explains the disappearance of local chromatin organization. These processes are dynamic, and cells rapidly reconstitute their default chromatin conformation after stress removal, uncovering an intrinsic organization. Transcription is not required for local chromatin reorganization, while compartment recovery is partially transcription-dependent. Thus, nuclear organization in mammalian cells can be rapidly modulated by environmental changes in a reversible manner.
引用
收藏
页码:18 / 28
页数:11
相关论文
共 55 条
[1]   Chromatin domains and the interchromatin compartment form structurally defined and functionally interacting nuclear networks [J].
Albiez, Heiner ;
Cremer, Marion ;
Tiberi, Cinzia ;
Vecchio, Lorella ;
Schermelleh, Lothar ;
Dittrich, Sandra ;
Kuepper, Katrin ;
Joffe, Boris ;
Thormeyer, Tobias ;
von Hase, Johann ;
Yang, Siwei ;
Rohr, Karl ;
Leonhardt, Heinrich ;
Solovei, Irina ;
Cremer, Christoph ;
Fakan, Stanislav ;
Cremer, Thomas .
CHROMOSOME RESEARCH, 2006, 14 (07) :707-733
[2]  
[Anonymous], 2016, GGPLOT2 ELEGANT GRAP
[3]   Tracking rates of transcription and splicing in vivo [J].
Ardehali, M. Behfar ;
Lis, John T. .
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2009, 16 (11) :1123-1124
[4]   Multiscale 3D Genome Rewiring during Mouse Neural Development [J].
Bonev, Boyan ;
Cohen, Netta Mendelson ;
Szabo, Quentin ;
Fritsch, Lauriane ;
Papadopoulos, Giorgio L. ;
Lubling, Yaniv ;
Xu, Xiaole ;
Lv, Xiaodan ;
Hugnot, Jean-Philippe ;
Tanay, Amos ;
Cavalli, Giacomo .
CELL, 2017, 171 (03) :557-+
[5]  
Brocker Chad, 2012, Biomol Concepts, V3, P345
[6]   Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl [J].
Busslinger, Georg A. ;
Stocsits, Roman R. ;
van der Lelij, Petra ;
Axelsson, Elin ;
Tedeschi, Antonio ;
Galjart, Niels ;
Peters, Jan-Michael .
NATURE, 2017, 544 (7651) :503-+
[7]   Progesterone receptor blockade in human breast cancer cells decreases cell cycle progression through G2/M by repressing G2/M genes [J].
Clare, Susan E. ;
Gupta, Akash ;
Choi, MiRan ;
Ranjan, Manish ;
Lee, Oukseub ;
Wang, Jun ;
Ivancic, David Z. ;
Kim, J. Julie ;
Khan, Seema A. .
BMC CANCER, 2016, 16
[8]   Condensin-driven remodelling of X chromosome topology during dosage compensation [J].
Crane, Emily ;
Bian, Qian ;
McCord, Rachel Patton ;
Lajoie, Bryan R. ;
Wheeler, Bayly S. ;
Ralston, Edward J. ;
Uzawa, Satoru ;
Dekker, Job ;
Meyer, Barbara J. .
NATURE, 2015, 523 (7559) :240-U299
[9]   Topology of mammalian developmental enhancers and their regulatory landscapes [J].
de Laat, Wouter ;
Duboule, Denis .
NATURE, 2013, 502 (7472) :499-506
[10]   Controlling gene expression in response to stress [J].
de Nadal, Eulalia ;
Ammerer, Gustav ;
Posas, Francesc .
NATURE REVIEWS GENETICS, 2011, 12 (12) :833-845