Topology, structures, and energy landscapes of human chromosomes

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 19, 2015, Pages 6062-6067

  Zhang, Bin ^a   Wolynes, Peter G ^a  

^a RICE UNIVERSITY   (United States)

Author keywords

Chromosome conformation capture; Liquid crystal; Maximum entropy; Topologically associating domains

Indexed keywords

ARTICLE; CHROMOSOME STRUCTURE; CONFORMATION; DYNAMICS; ENERGY; ENTROPY; FIBER; HUMAN; HUMAN CHROMOSOME; INTERPHASE; PRIORITY JOURNAL; CELL DIFFERENTIATION; CHEMICAL STRUCTURE; CHEMISTRY; CHROMATIN; CHROMOSOME; GENE EXPRESSION REGULATION; GENETICS; HUMAN GENOME; PROBABILITY; THERMODYNAMICS;

CHROMATIN; DNA;

CELL DIFFERENTIATION; CHROMATIN; CHROMOSOMES; CHROMOSOMES, HUMAN; DNA; GENE EXPRESSION REGULATION; GENOME, HUMAN; HUMANS; INTERPHASE; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROBABILITY; THERMODYNAMICS;

EID: 84929190426     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1506257112     Document Type: Article

References (50)

1. Misteli T (2007) Beyond the sequence: Cellular organization of genome function. Cell 128(4):787-800.
2. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG (1995) Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins 21(3):167-195.
3. Frauenfelder H, Sligar SG, Wolynes PG (1991) The energy landscapes and motions of proteins. Science 254(5038):1598-1603.
4. Wolynes PG (December 18, 2014) Evolution, energy landscapes and the paradoxes of protein folding. Biochimie, 10.1016/j.biochi.2014.12.007.
5. Marko JF (2008) Micromechanical studies of mitotic chromosomes. Chromosome Res 16(3):469-497.
6. Finch JT, Klug A (1976) Solenoidal model for superstructure in chromatin. Proc Natl Acad Sci USA 73(6):1897-1901.
7. Ong C-T, Corces VG (2014) CTCF: An architectural protein bridging genome topology and function. Nat Rev Genet 15(4):234-246.
8. Grosberg A, Rabin Y, Havlin S, Neer A (1993) Crumpled globule model of the three-dimensional structure of DNA. Europhys Lett 23(5):373.
9. Rosa A, Everaers R (2008) Structure and dynamics of interphase chromosomes. PLOS Comput Biol 4(8):e1000153.
10. Naumova N, et al. (2013) Organization of the mitotic chromosome. Science 342(6161):948-953.
11. Phillips-Cremins JE, et al. (2013) Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 153(6):1281-1295.
12. Lieberman-Aiden E, et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950):289-293.
13. van Steensel B, Dekker J (2010) Genomics tools for unraveling chromosome architecture. Nat Biotechnol 28(10):1089-1095.
14. Tokuda N, Terada TP, Sasai M (2012) Dynamical modeling of three-dimensional genome organization in interphase budding yeast. Biophys J 102(2):296-304.
15. Umbarger MA, et al. (2011) The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell 44(2):252-264.
16. Duan Z, et al. (2010) A three-dimensional model of the yeast genome. Nature 465(7296):363-367.
17. O'Sullivan JM, Hendy MD, Pichugina T, Wake GC, Langowski J (2013) The statistical-mechanics of chromosome conformation capture. Nucleus 4(5):390-398.
18. Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L (2012) Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol 30(1):90-98.
19. Giorgetti L, et al. (2014) Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell 157(4):950-963.
20. Nagano T, et al. (2013) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502(7469):59-64.
21. Wang S, Wolynes PG (2011) Communication: Effective temperature and glassy dynamics of active matter. J Chem Phys 135(5):051101.
22. Wang S, Wolynes PG (2012) Tensegrity and motor-driven effective interactions in a model cytoskeleton. J Chem Phys 136(14):145102.
23. Swedlow JR, Sedat JW, Agard DA (1993) Multiple chromosomal populations of topoisomerase II detected in vivo by time-lapse, three-dimensional wide-field microscopy. Cell 73(1):97-108.
24. Pitera JW, Chodera JD (2012) On the use of experimental observations to bias simulated ensembles. J Chem Theory Comput 8(10):3445-3451.
25. Roux B, Weare J (2013) On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method. J Chem Phys 138(8):084107.
26. Savelyev A, Papoian GA (2009) Molecular renormalization group coarse-graining of electrolyte solutions: Application to aqueous NaCl and KCl. J Phys Chem B 113(22):7785-7793.
27. Dixon JR, et al. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485(7398):376-380.
28. Mirny LA (2011) The fractal globule as a model of chromatin architecture in the cell. Chromosome Res 19(1):37-51.
29. Mateos-Langerak J, et al. (2009) Spatially confined folding of chromatin in the interphase nucleus. Proc Natl Acad Sci USA 106(10):3812-3817.
30. Robinson PJJ, Fairall L, Huynh VAT, Rhodes D (2006) EM measurements define the dimensions of the "30-nm" chromatin fiber: Evidence for a compact, interdigitated structure. Proc Natl Acad Sci USA 103(17):6506-6511.
31. Fisher CL, Fisher AG (2011) Chromatin states in pluripotent, differentiated, and reprogrammed cells. Curr Opin Genet Dev 21(2):140-146.
32. Cremer T, Cremer M (2010) Chromosome territories. Cold Spring Harb Perspect Biol 2(3):a003889.
33. Champoux JJ (2001) DNA topoisomerases: Structure, function, and mechanism. Annu Rev Biochem 70:369-413.
34. Barbieri M, et al. (2012) Complexity of chromatin folding is captured by the strings and binders switch model. Proc Natl Acad Sci USA 109(40):16173-16178.
35. Bohn M, Heermann DW (2010) Diffusion-driven looping provides a consistent framework for chromatin organization. PLoS ONE 5(8):e12218.
36. Gürsoy G, Xu Y, Kenter AL, Liang J (2014) Spatial confinement is a major determinant of the folding landscape of human chromosomes. Nucleic Acids Res 42(13):8223-8230.
37. Grosberg A, Khokhlov A (1994) Statistical Physics of Macromolecules (AIP, Woodbury, NY).
38. Frank-KamenetskiѤ MD, VologodskiѤ AV (1981) Topological aspects of the physics of polymers: The theory and its biophysical applications. Sov Phys Usp 24(8):679.
39. Sikorav JL, Jannink G (1994) Kinetics of chromosome condensation in the presence of topoisomerases: A phantom chain model. Biophys J 66(3 Pt 1):827-837.
40. Weinkam P, Pletneva EV, Gray HB, Winkler JR, Wolynes PG (2009) Electrostatic effects on funneled landscapes and structural diversity in denatured protein ensembles. Proc Natl Acad Sci USA 106(6):1796-1801.
41. Shoemaker BA, Wolynes PG (1999) Exploring structures in protein folding funnels with free energy functionals: The denatured ensemble. J Mol Biol 287(3):657-674.
42. Kireeva N, Lakonishok M, Kireev I, Hirano T, Belmont AS (2004) Visualization of early chromosome condensation: A hierarchical folding, axial glue model of chromosome structure. J Cell Biol 166(6):775-785.
43. Stillinger FH, Weber TA (1982) Hidden structure in liquids. Phys Rev A 25:978-989.
44. Gautier A, Michel-Salamin L, Tosi-Couture E, McDowall AW, Dubochet J (1986) Electron microscopy of the chromosomes of dinoflagellates in situ: Confirmation of Bouligand's liquid crystal hypothesis. J Ultrastruct Mol Struct Res 97:10-30.
45. Nishino Y, et al. (2012) Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure. EMBO J 31(7):1644-1653.
46. Nora EP, Dekker J, Heard E (2013) Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods? BioEssays 35(9):818-828.
47. Luthey-Schulten Z, Ramirez BE, Wolynes PG (1995) Helix-coil, liquid crystal, and spin glass transitions of a collapsed heteropolymer. J Phys Chem 99(7):2177-2185.
48. Sasai M, Wolynes PG (2003) Stochastic gene expression as a many-body problem. Proc Natl Acad Sci USA 100(5):2374-2379.
49. Zhang B, Wolynes PG (2014) Stem cell differentiation as a many-body problem. Proc Natl Acad Sci USA 111(28):10185-10190.
50. Sasai M, Kawabata Y, Makishi K, Itoh K, Terada TP (2013) Time scales in epigenetic dynamics and phenotypic heterogeneity of embryonic stem cells. PLOS Comput Biol 9(12):e1003380.