Complexity of chromatin folding is captured by the strings and binders switch model

被引:380
作者
Barbieri, Mariano [2 ,3 ]
Chotalia, Mita [1 ]
Fraser, James [4 ,5 ]
Lavitas, Liron-Mark [1 ]
Dostie, Josee [4 ,5 ]
Pombo, Ana [1 ]
Nicodemi, Mario [2 ,3 ]
机构
[1] Univ London Imperial Coll Sci Technol & Med, Genome Funct Grp, MRC, Ctr Clin Sci, London W12 0NN, England
[2] Univ Naples Federico II, Dipartimento Sci Fis, I-80126 Naples, Italy
[3] Complesso Univ Monte St Angelo, Ist SPIN, Ctr Nazl Ric, Ist Nazl Fis Nucl,Sez Napoli, I-80126 Naples, Italy
[4] McGill Univ, Dept Biochem, Montreal, PQ H3G 1Y6, Canada
[5] McGill Univ, Goodman Canc Res Ctr, Montreal, PQ H3G 1Y6, Canada
基金
加拿大健康研究院; 英国医学研究理事会;
关键词
genome organization; genome architecture; long-range chromatin interactions; fluorescence in situ hybridization; Monte Carlo simulations; CHROMOSOME TERRITORIES; INTERPHASE CHROMOSOMES; ORGANIZATION; GENOME; TRANSCRIPTION; NUCLEI; COLOCALIZATION; ARCHITECTURE; PRINCIPLES; SEQUENCE;
D O I
10.1073/pnas.1204799109
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Chromatin has a complex spatial organization in the cell nucleus that serves vital functional purposes. A variety of chromatin folding conformations has been detected by single-cell imaging and chromosome conformation capture-based approaches. However, a unified quantitative framework describing spatial chromatin organization is still lacking. Here, we explore the "strings and binders switch" model to explain the origin and variety of chromatin behaviors that coexist and dynamically change within living cells. This simple polymer model recapitulates the scaling properties of chromatin folding reported experimentally in different cellular systems, the fractal state of chromatin, the processes of domain formation, and looping out. Additionally, the strings and binders switch model reproduces the recently proposed "fractal-globule" model, but only as one of many possible transient conformations.
引用
收藏
页码:16173 / 16178
页数:6
相关论文
共 37 条
[1]   Global Chromatin Architecture Reflects Pluripotency and Lineage Commitment in the Early Mouse Embryo [J].
Ahmed, Kashif ;
Dehghani, Hesam ;
Rugg-Gunn, Peter ;
Fussner, Eden ;
Rossant, Janet ;
Bazett-Jones, David P. .
PLOS ONE, 2010, 5 (05)
[2]   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
[3]   Polycomb group proteins: repression in 3D [J].
Bantignies, Frederic ;
Cavalli, Giacomo .
TRENDS IN GENETICS, 2011, 27 (11) :454-464
[4]   Random loop model for long polymers [J].
Bohn, Manfred ;
Heermann, Dieter W. ;
van Driel, Roel .
PHYSICAL REVIEW E, 2007, 76 (05)
[5]   Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization [J].
Bohn, Manfred ;
Heermann, Dieter W. .
PLOS ONE, 2010, 5 (08)
[6]   Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations [J].
Branco, Miguel R. ;
Pombo, Ana .
PLOS BIOLOGY, 2006, 4 (05) :780-788
[7]   Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription [J].
Chambeyron, S ;
Bickmore, WA .
GENES & DEVELOPMENT, 2004, 18 (10) :1119-1130
[8]   Molecular biology - The organization of replication and transcription [J].
Cook, PR .
SCIENCE, 1999, 284 (5421) :1790-1795
[9]   Chromosome territories, nuclear architecture and gene regulation in mammalian cells [J].
Cremer, T ;
Cremer, C .
NATURE REVIEWS GENETICS, 2001, 2 (04) :292-301
[10]  
De Gennes P.-G, 1979, Scaling concepts in polymer physics