"Entropic organization of interphase chromosomes".

Peter R. Cook ¹ and Davide Marenduzzo ²

¹ Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, England, UK
² Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3JZ, Scotland, UK

Correspondence to Peter R. Cook: peter.cook@path.ox.ac.uk

Chromosomes are not distributed randomly in nuclei. Appropriate positioning can activate (or repress) genes by bringing them closer to active (or inactive) compartments like euchromatin (or heterochromatin), and this is usually assumed to be driven by specific local forces (e.g., involving H bonds between nucleosomes or between nucleosomes and the lamina). Using Monte Carlo simulations, we demonstrate that nonspecific (entropic) forces acting alone are sufficient to position and shape self-avoiding polymers within a confining sphere in the ways seen in nuclei. We suggest that they can drive long flexible polymers (representing gene-rich chromosomes) to the interior, compact/thick ones (and heterochromatin) to the periphery, looped (but not linear) ones into appropriately shaped (ellipsoidal) territories, and polymers with large terminal beads (representing centromeric heterochromatin) into peripheral chromocenters. Flexible polymers tend to intermingle less than others, which is in accord with observations that gene-dense (and so flexible) chromosomes make poor translocation partners. Thus, entropic forces probably participate in the self-organization of chromosomes within nuclei.

Additional references:

1. Hovsepian JA, and Frenster JH,  (2003b)
"Euchromatin as an Extensile Force within Mammalian Cell Nuclei".

2. Hovsepian JA, and Frenster JH,  (2003c)
"Bioassays of Isolated Nuclear RNA Species as Activators of DNA Transcription".

3. Frenster JH, and Hovsepian JA,  (2004a)
"Activator RNA Exchange during Interphase Chromatin Reprogramming".

4. Frenster JH, and Hovsepian JA,  (2004b)
"Ultrastructure  of Closed Loops within Euchromatin of Isolated Lymphocyte Nuclei".

5, Hovsepian JA, and Frenster JH,  (2004c)
"Reprogramming as an Approach to Neoplasms".

6. Hovsepian JA, and Frenster JH,  (2005a)
"Sense and Antisense during RNA Initiation of the DNA Transcription Bubble".

7. Frenster JH, and Hovsepian JA,  (2005b)
"Ultrastructure of Euchromatin Contact Points between the Closed Loops of Adjacent Interphase Chromosomes".

8 Frenster JH, and Hovsepian JA,  (2006a)
"Kissing Chromosomes and Paired Sense-Antisense RNA Synthesis".

9. 33b. Frenster JH, and Hovsepian JA,  (2006b)
"Activator RNA Initiation of the DNA Transcription Bubble".

10. Hovsepian JA, and Frenster JH,  (2006c)
"Chromosome-Chromosome Contact Points and Paired Sense-Antisense RNA Synthesis".

11. Frenster JH, and Hovsepian JA,  (2006d)
"DNase-I Ultrastructural Probe Sites and Kissing Chromosomes".

12. Frenster JH, and Hovsepian JA, (2008b)
"Models of successive levels of resolution during individual gene transcription".
 

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PMID: 1988281 [PubMed - indexed for MEDLINE]

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78:

Origins of structure in globular proteins.

Chan HS, Dill KA.

Proc Natl Acad Sci U S A. 1990 Aug;87(16):6388-92.

PMID: 2385597 [PubMed - indexed for MEDLINE]

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79:

Distribution of chromosome 18 and X centric heterochromatin in the interphase nucleus of cultured human cells.

Popp S, Scholl HP, Loos P, Jauch A, Stelzer E, Cremer C, Cremer T.

Exp Cell Res. 1990 Jul;189(1):1-12.

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80:

The effects of chromosome rearrangements on the expression of heterochromatic genes in chromosome 2L of Drosophila melanogaster.

Wakimoto BT, Hearn MG.

Genetics. 1990 May;125(1):141-54.

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81:

[Chromocenters of interphase nuclei in the mouse liver contain satellite DNA]

Stefanova EV, Chentsov IuS.

Mol Biol (Mosk). 1990 Mar-Apr;24(2):501-5. Russian.

PMID: 1694569 [PubMed - indexed for MEDLINE]

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82:

Three-dimensional analysis of the organization of human chromosome domains in human and human-hamster hybrid interphase nuclei.

van Dekken H, Pinkel D, Mullikin J, Trask B, van den Engh G, Gray J.

J Cell Sci. 1989 Oct;94 ( Pt 2):299-306.

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83:

Large-scale chromatin structural domains within mitotic and interphase chromosomes in vivo and in vitro.

Belmont AS, Braunfeld MB, Sedat JW, Agard DA.

Chromosoma. 1989 Aug;98(2):129-43.

PMID: 2476279 [PubMed - indexed for MEDLINE]

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84:

Double in situ hybridization in combination with digital image analysis: a new approach to study interphase chromosome topography.

Emmerich P, Loos P, Jauch A, Hopman AH, Wiegant J, Higgins MJ, White BN, van der Ploeg M, Cremer C, Cremer T.

Exp Cell Res. 1989 Mar;181(1):126-40.

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85:

Molecular cytological differentiation of active from inactive X domains in interphase: implications for X chromosome inactivation.

Dyer KA, Canfield TK, Gartler SM.

Cytogenet Cell Genet. 1989;50(2-3):116-20.

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86:

Transcriptional activity of constitutive heterochromatin in the mammal Microtus agrestis (Rodentia, Cricetidae).

Sperling K, Kalscheuer V, Neitzel H.

Exp Cell Res. 1987 Dec;173(2):463-72.

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87:

Three-dimensional organization of Drosophila melanogaster interphase nuclei. I. Tissue-specific aspects of polytene nuclear architecture.

Hochstrasser M, Sedat JW.

J Cell Biol. 1987 Jun;104(6):1455-70.

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88:

DNA sequence adjacent to and specific for the 1.672 g/cm3 satellite DNA in the Drosophila genome.

Donnelly RJ, Kiefer BI.

Proc Natl Acad Sci U S A. 1986 Oct;83(19):7172-6.

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89:

Rearrangements of chromosomal regions containing ribosomal RNA genes and centromeric heterochromatin in the human melanoma cell line MeWo.

Holden JJ, Reimer DL, Roder JC, White BN.

Cancer Genet Cytogenet. 1986 Apr 1;21(3):221-37.

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90:

The fine structure of euchromatin and centromeric heterochromatin in Tenebrio molitor chromosomes.

Weith A.

Chromosoma. 1985;91(3-4):287-96.

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91:

NOR associations with heterochromatin.

Tuck-Muller CM, Bordson BL, Varela M, Bennett JW.

Cytogenet Cell Genet. 1984;38(3):165-70.

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92:

Cytofluorometric DNA base determination for the investigation of heterochromatin and heterochromatin amplification.

Leemann U, Ruch F.

Exp Cell Res. 1983 Sep;147(2):419-29.

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93:

Association of centromeric heterochromatin with the nucleolus in mouse Sertoli cells.

Jean P, Hartung M, Mirre C, Stahl A.

Anat Rec. 1983 Apr;205(4):375-80.

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94:

Heterochromatin markers: arrangement of obligatory heterochromatin, histone genes and multisite gene families in the interphase nucleus of D. melanogaster.

Lifschytz E, Hareven D.

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95:

[Structural characteristics of the centromeric heterochromatin of mice]

Burakov VV, Onishchenko GE, Chentsov IuS.

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96:

Fluorescence patterns of heterochromatin in mitotic and polytene chromosomes in seven members of three sub-groups of the melanogaster species group of Drosophila.

Lakhotia SC, Mishra A.

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97:

Cell cycle dependent changes of chromosomes in mouse fibroblasts.

Moser GC, Müller H.

Eur J Cell Biol. 1979 Jun;19(2):116-9.

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98:

Localization of Drosophila nasutoides satellite DNAs in metaphase chromosomes.

Wheeler LL, Arrighi F, Cordeiro-Stone M, Lee CS.

Chromosoma. 1978 Dec 21;70(1):41-50.

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99:

Heterochromatin in mitotic chromosomes of Drosophila nasuta.

Lakhotia SC, Kumar M.

Cytobios. 1978;21(82):79-89.

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100:

Leucocyte morphology and chromosome morphology.

Dallapiccola B, Baricordi O, Capra L, Mazzilli C.

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101:

Hoechst 33258 fluorescent staining of Drosophila chromosomes.

Holmquist G.

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