The nuclear physique

International Review of Cell and Molecular Biology

Volumn 307, Issue , 2014, Pages 1-13

  Pederson, Thoru ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

Biophysics; Nuclear organization; Nucleus; Physical cell biology

Indexed keywords

GREEN FLUORESCENT PROTEIN; NUCLEAR PROTEIN;

ARTICLE; CELL NUCLEUS; CELL NUCLEUS INCLUSION BODY; CELL NUCLEUS MATRIX; CELL NUCLEUS MEMBRANE; CHROMOSOME BREAKAGE; CHROMOSOME SIZE; CYTOLOGY; DNA REPAIR; FLUORESCENCE CORRELATION SPECTROSCOPY; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; INTERPHASE; MACROMOLECULAR CROWDING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN STRUCTURE;

BIOPHYSICS; NUCLEAR ORGANIZATION; NUCLEUS; PHYSICAL CELL BIOLOGY;

ANIMALS; BIOPHYSICAL PROCESSES; CELL NUCLEUS; HUMANS;

EID: 84891118506     PISSN: 19376448     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-800046-5.00001-1     Document Type: Chapter

References (60)

1. Anderson P.W. More is different. Science 1972, 177:393-396.
2. Bancaud A., et al. Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin. EMBO J. 2009, 28:3785-3798.
3. Belin B.J., et al. Visualization of actin filaments and monomers in somatic cell nuclei. Mol. Biol. Cell 2013, 24:982-994.
4. Belmont A.S. Estrogen fueled, nuclear kiss. Did it move for youα. Nucleus 2010, 1:440-443.
5. Brangwynne C.P., et al. Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:4334-4349.
6. Brown A. J.D. Bernal. The Sage of Science 2005, Oxford University Press, Oxford, U.K.
7. Canals-Hamann A.Z., et al. A biophysical model for transcription factories. BMC Biophys. 2013, 6:2-6.
8. Celedon A., Hale C.M., Wirtz D. Magnetic manipulation of nanorods in the nucleus of living cells. Biophys. J. 2011, 101:1880-1886.
9. Cremer T., et al. Analysis of chromosome positions in the interphase nucleus of Chinese hamster cells by laser-UV-microirradiation experiments. Hum. Genet. 1982, 62:201-209.
10. Crick F.H.C. The physical properties of cytoplasm. A study by means of the magnetic particle method. Part II. Theoretical treatment. Exp. Cell Res. 1950, 1:505-533.
11. Crick F.H.C., Hughes A.F.W. The physical properties of cytoplasm. A study by means of the magnetic particle method. Part I. Experimental. Exp. Cell Res. 1950, 1:37-60.
12. Dekker J., Marti-Remon M.A., Mirny L.A. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat. Rev. Genet. 2013, 14:390-403.
13. Dundr M., et al. A kinetic framework for a mammalian RNA polymerase in vivo. Science 2002, 298:1623-1626.
14. Ellis R.J., Minton A.P. Join the crowd. Nature 2003, 425:27-28.
15. Farquharson A.S.L. Movement of animals. Bollingen Series LXXI 1984, vol. 1:1087-1096. Princeton University Press, Princeton, NJ, (Revised Oxford translation). J. Barnes (Ed.).
16. Funkhouser C.M., et al. Mechanical model of blebbing in nuclear lamin meshworks. Proc. Natl. Acad. Sci. U. S. A. 2013, 110:3248-3253.
17. Grunwald D., et al. Probing intranuclear environments at the single-molecule level. Biophys. J. 2008, 94:2847-2858.
18. Grunwald D., Singer R.H., Rout M.P. Nuclear export dynamics of RNA-protein complexes. Nature 2011, 475:333-341.
19. Hancock R. A role for macromolecular crowding effects in the assembly and function of compartments in the nucleus. J. Struct. Biol. 2004, 146:281-290.
20. Hancock R. Packing of the polynucleosomne chain in interphase chromosomes. Evidence for a contribution of crowding and entropic forces. Semin. Cell Dev. Biol. 2007, 18:668-675.
21. Holmes F.L. Meselson, Stahl, and the Replication of DNA. A History of "The Most Beautiful Experiment in Biology" 2001, Yale University Press, New Haven, CT.
22. Houtsmuller A., et al. Action of DNA repair endonuclease ERCC/XPF in living cells. Science 1999, 284:958-961.
23. Hu Q., et al. Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:19199-19204.
24. Iborra F.J. Can visco-elastic phase separation, macromolecular crowding and colloidal physics explain nuclear organizationα. Theor. Biol. Med. Model. 2007, 4:15.
25. Kaiser T.E., Intine R.V., Dundr M. De novo formation of a subnuclear body. Science 2008, 322:1713-1717.
26. Kocanova S., et al. Activation of estrogen-responsive genes does not require their nuclear co-localization. PLoS Genet. 2010, 6:1000922.
27. Kues T., et al. Visualization and tracking of single protein molecules in the cell nucleus. Biophys. J. 2001, 80:2954-2967.
28. Larson D.R., et al. Real-time observation of transcription initiation and elongation on an endogenous yeat gene. Science 2011, 332:475-478.
29. Lin S., Riggs A.D. The general affinity of lac repressor for E. coli DNA: implications for gene regulation in prokaryotes and eucaryotes. Cell 1975, 4:107-111.
30. Marko J.F. The liquid drop nature of nucleoli. Nucleus 2012, 3:115-117.
31. Marshall W.F., et al. Interphase chromosomes undergo constrained diffusional motion in living cells. Curr. Biol. 1997, 7:930-939.
32. McDonald D., et al. Nucleoplasmic beta-actin exists in a dynamic equilibrium between low-mobility polymeric species and rapidly diffusing populations. J. Cell Biol. 2006, 172:541-552.
33. Mor A., Ben-Yishay R., Shav-Tal Y. On the right track: following the nucleo-cytoplasmic path of an mRNA. Nucleus 2010, 1:492-498.
34. O'Brien T.P., et al. Genome function and nuclear architecture: from gene expression to nanoscience. Genome Res. 2003, 13:1029-1041.
35. Pederson T. Thinking about a nuclear matrix. J. Mol. Biol. 1998, 277:147-159.
36. Pederson T. Half a century of "the nuclear matrix". Mol. Biol. Cell 2000, 11:799-805.
37. Pederson T. Diffusional transport in the nucleus: a message in the medium. Nat. Cell Biol. 2000, 2:E73-E74.
38. Pederson T. Protein mobility within the nucleus-what are the right movesα. Cell 2001, 104:635-638.
39. Pederson T. Gene territories and cancer. Nat. Genet. 2003, 34:4-5.
40. Pederson T. The spatial organization of the genome in mammalian cells. Curr. Opin. Genet. Dev. 2004, 14:203-209.
41. Pederson T. As functional nuclear actin comes into view, is it globular, filamentous, or bothα. J. Cell Biol. 2008, 180:1061-1064.
42. Pederson T. The nucleus introduced. The Nucleus 2010, 1-16. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. T. Misteli, D.L. Spector (Eds.).
43. Pederson T. The nucleolus. The Nucleus 2010, 209-223. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. T. Misteli, D.L. Spector (Eds.).
44. Pederson T. Nuclear export, enlightened. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:9228-9229.
45. Politz J.C., Pederson T. Movement of mRNA from transcription site to nuclear pores. J. Struct. Biol. 2000, 129:252-257.
46. Politz J.C., et al. Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy. Proc. Natl. Acad. Sci. U. S. A. 1998, 95:6043-6048.
47. Politz J.C., et al. Movement of poly(A) RNA throughout the interchromatin space in living cells. Curr. Biol. 1999, 9:285-291.
48. Politz J.C., Tuft R.A., Pederson T. Diffusion-based transport of nascent ribosomes in the nucleus. Mol. Biol. Cell 2003, 14:4805-4812.
49. Richter K., Neesling M., Lichter P. Macromolecular crowding and its potential impact on nuclear function. Biochim. Biophys. Acta 2008, 1783:2100-2107.
50. Robbins E., Pederson T., Klein P. Comparison of mitotic phenomena and effects induced by hypertonic solutions in HeLa cells. J. Cell Biol. 1970, 44:400-416.
51. Robertson, E., 2007. Music and lyrics. Theme for "The Big Bang Theory" television show.
52. Rowat A.C., et al. Characterization of the elastic properties of the nuclear envelope. J. R. Soc. Interface. 2005, 2:63-69.
53. Rowat A.C., Lammerling J., Ipsen J.H. Mechanical properties of the cell nucleus and the effect of emerin deficiency. Biophys. J. 2006, 91:4649-4664.
54. Schneider D.A., Nomura M. RNA polymerase I remains intact without subunit exchange through multiple rounds of transcription in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:15112-15117.
55. Siebrasse J.P., Kaminski T., Kubitscheck U. Nuclear export of single native mRNA molecules observed by light sheet fluorescence microscopy. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:9426-9431.
56. Tjong H. Physical tethering and volume exclusion determine higher-order genome organization in budding yeast. Genome Res. 2012, 22:1295-1305.
57. Tseng Y., et al. Micro-organization and visco-elasticity of the interphase nucleus revealed by particle tracking. J. Cell Sci. 2004, 117:2159-2167.
58. Tu S., Pederson T., Weng Z. Networking development by Boolean logic. Nucleus 2013, 4:89-91.
59. Wachsmuth M., Waldeck W., Langowski J. Anomalous diffusion of fluoresecent probes inside living cell nuclei investigated by spatially resolved fluorescence correlation spectroscopy. J. Mol. Biol. 2000, 298:677-689.
60. Wedemeier A., et al. Modeling diffusional transport in the interphase cell nucleus. J. Chem. Phys. 2007, 127:045102.