The role of loops on the order of eukaryotes and prokaryotes

FEBS Letters

Volumn 589, Issue 20, 2015, Pages 2958-2965

  Hofmann, Andreas ^a   Heermann, Dieter W ^a,b,c,d  

^a INSTITUT FÜR THEORETISCHE PHYSIK   (Germany)

^b JACKSON LABORATORY   (United States)

^c Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^d SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

Author keywords

Chromatin looping; Polymer modeling; Topological domain

Indexed keywords

DNA; CHROMATIN;

ARTICLE; CHROMATIN; CHROMOSOME STRUCTURE; CONFORMATIONAL TRANSITION; CROSS LINKING; ENHANCER REGION; EUKARYOTE; GENE FREQUENCY; GENE INTERACTION; GENETIC DISTANCE; MICROBIAL GENETICS; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PROMOTER REGION; SIMULATION; ANIMAL; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BIOLOGICAL MODEL; CELL NUCLEUS; CONFORMATION; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENETICS; HUMAN; PHYSIOLOGY; ULTRASTRUCTURE;

ANIMALS; CELL NUCLEUS; CHROMATIN; CHROMOSOMES, BACTERIAL; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; HUMANS; MODELS, GENETIC; NUCLEIC ACID CONFORMATION;

EID: 84943361248     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2015.04.021     Document Type: Review

References (69)

1. Johan H. Gibcus, and Job Dekker The hierarchy of the 3D genome Mol. Cell 49 5 2013 773 782
2. Wendy A. Bickmore, and Bas van Steensel Genome architecture: domain organization of interphase chromosomes Cell 152 6 2013 1270 1284
3. T. Cremer, and C. Cremer Chromosome territories, nuclear architecture and gene regulation in mammalian cells Nat. Rev. Genet. 2 4 2001 292 301
4. Erez Lieberman-Aiden, Nynke L. van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R. Lajoie, Peter J. Sabo, Michael O. Dorschner, Richard Sandstrom, Bradley Bernstein, M.A. Bender, Mark Groudine, Andreas Gnirke, John Stamatoyannopoulos, Leonid A. Mirny, Eric S. Lander, and Job Dekker Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 5950 2009 289 293
5. Jesse R. Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Hu Ming, Jun S. Liu, and Bing Ren Topological domains in mammalian genomes identified by analysis of chromatin interactions Nature 485 7398 2012 376 380
6. Elphège P. Nora, Bryan R. Lajoie, Edda G. Schulz, Luca Giorgetti, Ikuhiro Okamoto, Nicolas Servant, Tristan Piolot, Nynke L. van Berkum, Johannes Meisig, John Sedat, Joost Gribnau, Emmanuel Barillot, Nils Blüthgen, Job Dekker, and Edith Heard Spatial partitioning of the regulatory landscape of the x-inactivation centre Nature 485 7398 2012 381 385
7. Tom Sexton, Eitan Yaffe, Ephraim Kenigsberg, Frédéric Bantignies, Benjamin Leblanc, Michael Hoichman, Hugues Parrinello, Amos Tanay, and Giacomo Cavalli Three-dimensional folding and functional organization principles of the drosophila genome Cell 148 3 2012 458 472
8. Takashi Nagano, Yaniv Lubling, Tim J. Stevens, Stefan Schoenfelder, Eitan Yaffe, Wendy Dean, Ernest D. Laue, Amos Tanay, and Peter Fraser Single-cell Hi-C reveals cell-to-cell variability in chromosome structure Nature 502 7469 2013 59 64
9. Remus T. Dame, Olga J. Kalmykowa, and David C. Grainger Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria PLoS Genet. 7 6 2011 e1002123
10. Hironori Niki, Yoshiharu Yamaichi, and Sota Hiraga Dynamic organization of chromosomal DNA in Escherichia coli Genes Dev. 14 2 2000 212 223
11. Michèle Valens, Stéphanie Penaud, Michèle Rossignol, François Cornet, and Frédéric Boccard Macrodomain organization of the Escherichia coli chromosome EMBO J. 23 21 2004 4330 4341
12. Lisa Postow, Christine D. Hardy, Javier Arsuaga, and Nicholas R. Cozzarelli Topological domain structure of the Escherichia coli chromosome Genes Dev. 18 14 2004 1766 1779
13. Tung B.K. Le, Maxim V. Imakaev, Leonid A. Mirny, and Michael T. Laub High-resolution mapping of the spatial organization of a bacterial chromosome Science 342 6159 2013 731 734
14. Yin Shen, Feng Yue, David F. McCleary, Zhen Ye, Lee Edsall, Samantha Kuan, Ulrich Wagner, Jesse Dixon, Leonard Lee, Victor V. Lobanenkov, and Bing Ren A map of the cis-regulatory sequences in the mouse genome Nature 488 7409 2012 116 120
15. Andrea Smallwood, and Bing Ren Genome organization and long-range regulation of gene expression by enhancers Curr. Opin. Cell Biol. 25 3 2013 387 394
16. Bas Tolhuis, Robert-Jan Palstra, Erik Splinter, Frank Grosveld, and Wouter de Laat Looping and interaction between hypersensitive sites in the active-globin locus Mol. Cell 10 6 2002 1453 1465
17. Takanori Amano, Tomoko Sagai, Hideyuki Tanabe, Yoichi Mizushina, Hiromi Nakazawa, and Toshihiko Shiroishi Chromosomal dynamics at the shh locus: limb bud-specific differential regulation of competence and active transcription Dev. Cell 16 1 2009 47 57
18. Suhas S.P. Rao, Miriam H. Huntley, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, Ido Machol, Arina D. Omer, Eric S. Lander, and Erez Lieberman Aiden A 3d map of the human genome at kilobase resolution reveals principles of chromatin looping Cell 159 7 2014 1665 1680
19. Julio Mateos-Langerak, Manfred Bohn, Wim de Leeuw, Osdilly Giromus, Erik M.M. Manders, Pernette J. Verschure, Mireille H.G. Indemans, Hinco J. Gierman, Dieter W. Heermann, Roel van Driel, and Sandra Goetze Spatially confined folding of chromatin in the interphase nucleus Proc. Natl. Acad. Sci. 106 10 2009 3812 3817
20. Dieter W. Heermann Physical nuclear organization: loops and entropy Curr. Opin. Cell Biol. 23 3 2011 332 337
21. Manfred Bohn, and Dieter W. Heermann Diffusion-driven looping provides a consistent framework for chromatin organization PLoS One 5 8 2010 e12218
22. Yoko Ito, Raffaella Nativio, and Adele Murrell Induced DNA demethylation can reshape chromatin topology at the IGF2-h19 locus Nucl. Acids Res. 41 10 2013 5290 5302
23. Jennifer E. Phillips, and Victor G. Corces CTCF: master weaver of the genome Cell 137 7 2009 1194 1211
24. Jennifer E. Phillips-Cremins, Michael E.G. Sauria, Amartya Sanyal, Tatiana I. Gerasimova, Bryan R. Lajoie, Joshua S.K. Bell, Chin-Tong Ong, Tracy A. Hookway, Changying Guo, Yuhua Sun, Michael J. Bland, William Wagstaff, Stephen Dalton, Todd C. McDevitt, Ranjan Sen, Job Dekker, James Taylor, and Victor G. Corces Architectural protein subclasses shape 3d organization of genomes during lineage commitment Cell 153 6 2013 1281 1295
25. Mariliis Tark-Dame, Hansjoerg Jerabek, Erik M.M. Manders, Dieter W. Heermann, and Roel van Driel Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling PLoS Comput. Biol. 10 10 2014 e1003877
26. Yuanyuan Li, Weichun Huang, Liang Niu, David M. Umbach, Shay Covo, and Leping Li Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes BMC Genomics 14 1 2013 1 12
27. Jessica Zuin, Jesse R. Dixon, Michael I.J.A. van der Reijden, Zhen Ye, Petros Kolovos, Rutger W.W. Brouwer, Mariëtte P.C. van de Corput, Harmen J.G. van de Werken, Tobias A. Knoch, Wilfred F.J. van IJcken, Frank G. Grosveld, Bing Ren, and Kerstin S. Wendt Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells Proc. Natl. Acad. Sci. 111 3 2014 996 1001
28. Christian Lanctôt, Thierry Cheutin, Marion Cremer, Giacomo Cavalli, and Thomas Cremer Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions Nat. Rev. Genet. 8 2 2007 104 115
29. Fabrizio Benedetti, Julien Dorier, Yannis Burnier, and Andrzej Stasiak Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes Nucl. Acids Res. 42 5 2014 2848 2855
30. Catherine Naughton, Nicolaos Avlonitis, Samuel Corless, James G. Prendergast, Ioulia K. Mati, Paul P. Eijk, Scott L. Cockroft, Mark Bradley, Bauke Ylstra, and Nick Gilbert Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures Nat. Struct. Mol. Biol. 20 3 2013 387 395
31. Mariano Barbieri, Mita Chotalia, James Fraser, Liron-Mark Lavitas, Josée Dostie, Ana Pombo, and Mario Nicodemi Complexity of chromatin folding is captured by the strings and binders switch model Proc. Natl. Acad. Sci. 109 40 2012 16173 16178
32. Mario Nicodemi, and Ana Pombo Models of chromosome structure Curr. Opin. Cell Biol. 28 2014 90 95
33. Vittore F. Scolari, and Marco Cosentino Lagomarsino Combined collapse by bridging and self-adhesion in a prototypical polymer model inspired by the bacterial nucleoid Soft Matter 11 9 2015 1677 1687
34. Amartya Sanyal, Bryan R. Lajoie, Gaurav Jain, and Job Dekker The long-range interaction landscape of gene promoters Nature 489 7414 2012 109 113
35. Fulai Jin, Yan Li, Jesse R. Dixon, Siddarth Selvaraj, Zhen Ye, Ah Young Lee, Chia-An Yen, Anthony D. Schmitt, Celso A. Espinoza, and Bing Ren A high-resolution map of the three-dimensional chromatin interactome in human cells Nature 503 7475 2013 290 294
36. Manfred Bohn, Dieter W. Heermann, Odilon Lourenço, and Claudette Cordeiro On the influence of topological catenation and bonding constraints on ring polymers Macromolecules 43 5 2010 2564 2573
37. Boryana Doyle, Geoffrey Fudenberg, Maxim Imakaev, and Leonid A. Mirny Chromatin loops as allosteric modulators of enhancer-promoter interactions PLoS Comput. Biol. 10 10 2014 e1003867
38. Laura Baranello, Fedor Kouzine, and David Levens CTCF and cohesin cooperate to organize the 3d structure of the mammalian genome Proc. Natl. Acad. Sci. 111 3 2014 889 890
39. Matteo Vietri Rudan, Christopher Barrington, Stephen Henderson, Christina Ernst, Duncan T. Odom, Amos Tanay, and Suzana Hadjur Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture Cell Rep. 10 8 2015 1297 1309
40. Anton V. Persikov, and Mona Singh An expanded binding model for cys2his2 zinc finger protein-DNA interfaces Phys. Biol. 8 3 2011 035010
41. Lei Liu, and Dieter W. Heermann The interaction of DNA with multi-cys2his2 zinc finger proteins J. Phys. Condens. Matter 27 6 2015 064107
42. Remus T. Dame, Mariliis Tark-Dame, and Helmut Schiessel A physical approach to segregation and folding of the caulobacter crescentus genome Mol. Microbiol. 82 6 2011 1311 1315
43. Remus T. Dame The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin Mol. Microbiol. 56 4 2005 858 870
44. Ramon A. van der Valk, Jocelyne Vreede, Frédéric Crémazy, and Remus T. Dame Genomic looping: a key principle of chromatin organization J. Mol. Microbiol. Biotechnol. 24 5-6 2014 344 359
45. Martijn S. Luijsterburg, Malcolm F. White, Roel van Driel, and Remus Th. Dame The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes Crit. Rev. Biochem. Mol. Biol. 43 6 2008 393 418
46. Wenqin Wang, Gene-Wei Li, Chongyi Chen, X. Sunney Xie, and Xiaowei Zhuang Chromosome organization by a nucleoid-associated protein in live bacteria Science 333 6048 2011 1445 1449
47. Vlad C. Seitan, Andre J. Faure, Ye Zhan, Rachel Patton McCord, Bryan R. Lajoie, Elizabeth Ing-Simmons, Boris Lenhard, Luca Giorgetti, Edith Heard, Amanda G. Fisher, Paul Flicek, Job Dekker, and Matthias Merkenschlager Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments Genome Res. 23 12 2013 2066 2077
48. Sevil Sofueva, Eitan Yaffe, Wen-Ching Chan, Dimitra Georgopoulou, Matteo Vietri Rudan, Hegias Mira-Bontenbal, Steven M. Pollard, Gary P. Schroth, Amos Tanay, and Suzana Hadjur Cohesin-mediated interactions organize chromosomal domain architecture EMBO J. 32 24 2013 3119 3129
49. Job Dekker, Karsten Rippe, Martijn Dekker, and Nancy Kleckner Capturing chromosome conformation Science 295 5558 2002 1306 1311
50. Mariliis Tark-Dame, Roel van Driel, and Dieter W. Heermann Chromatin folding - from biology to polymer models and back J. Cell Sci. 124 6 2011 839 845
51. Hansjoerg Jerabek, and Dieter W. Heermann Expression-dependent folding of interphase chromatin PLoS One 7 5 2012 e37525
52. Axel Cournac, and Jacqueline Plumbridge DNA looping in prokaryotes: experimental and theoretical approaches J. Bacteriol. 195 6 2013 1109 1119
53. Pascal Reiss, Miriam Fritsche, and Dieter W. Heermann Looped star polymers show conformational transition from spherical to flat toroidal shapes Phys. Rev. E 84 5 2011 051910
54. Miriam Fritsche, Songling Li, Dieter W. Heermann, and Paul A. Wiggins A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation Nucl. Acids Res. 40 3 2011 972 980
55. Manfred Bohn, and Dieter W. Heermann Repulsive forces between looping chromosomes induce entropy-driven segregation PLoS One 6 1 2011 e14428
56. Davide Marenduzzo, Cristian Micheletti, and Peter R. Cook Entropy-driven genome organization Biophys. J. 90 10 2006 3712 3721
57. Peter R. Cook, and Davide Marenduzzo Entropic organization of interphase chromosomes J. Cell Biol. 186 6 2009 825 834
58. Suckjoon Jun, and Andrew Wright Entropy as the driver of chromosome segregation Nat. Rev. Microbiol. 8 8 2010 600 607
59. Miriam Fritsche, and Dieter W. Heermann Confinement driven spatial organization of semiflexible ring polymers: implications for biopolymer packaging Soft Matter 7 15 2011 6906 6913
60. Mariliis Tark-Dame, Martijn S. Luijsterburg, Dieter W. Heermann, and Roel van Driel Understanding genome function: quantitative modeling of chromatin folding and chromatin-associated processes Karsten Rippe, Genome Organization and Function in the Cell Nucleus 2011 Wiley-VCH Verlag GmbH & Co. KGaA 535 555
61. Suckjoon Jun, and Bela Mulder Entropy-driven spatial organization of highly confined polymers: lessons for the bacterial chromosome Proc. Natl. Acad. Sci. 103 33 2006 12388 12393
62. Barbara Di Ventura, Benoit Knecht, Helena Andreas, William J. Godinez, Miriam Fritsche, Karl Rohr, Walter Nickel, Dieter W. Heermann, and Victor Sourjik Chromosome segregation by the Escherichia coli min system Mol. Syst. Biol. 9 1 2013 686
63. Angelo Rosa, and Ralf Everaers Structure and dynamics of interphase chromosomes PLoS Comput. Biol. 4 8 2008 e1000153
64. John F. Marko Supercoiled and braided DNA under tension Phys. Rev. E 55 2 1997 1758 1772
65. Yang Zhang, Sebastian Isbaner, and Dieter W. Heermann Mechanics of sister chromatids studied with a polymer model Front. Phys. 1 2013 16
66. Dieter W. Heermann Mitotic chromosome structure Exp. Cell Res. 318 12 2012 1381 1385
67. I. Carmesin, and Kurt Kremer The bond fluctuation method: a new effective algorithm for the dynamics of polymers in all spatial dimensions Macromolecules 21 9 1988 2819 2823
68. H.P. Deutsch, and K. Binder Interdiffusion and self-diffusion in polymer mixtures: a monte carlo study J. Chem. Phys. 94 3 1991 2294
69. Alan D. Sokal Monte carlo methods in statistical mechanics: foundations and new algorithms Cecile DeWitt-Morette, Pierre Cartier, Antoine Folacci, Functional Integration: Basics and Applications, number 361 in NATO ASI Series 1997 Springer 131 192