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Three dimensional chromosome arrangements can affect genetics


A Darwinist was bugging a friend to provide peer-reviewed literature about the three-dimensional arrangement of chromosomes (the c-nome), that affects genetics. That Darwinist favours a one-dimensional arrangement (surprise, surprise).

He needs to get out more. From Jonathan Wells’ The Myth of Junk DNA (p. 79):

Between cell divisions, chromosomes are not randomly distributed in the nucleus. Instead, they occupy distinct domains [79-82] that affect gene regulation‹in part, by bringing together specific regions of the chromosomes and facilitating interactions among them. [83-88] Different cell and tissue types in the same animal can have different three-dimensional patterns of chromosomes in their nuclei, which account for at least some differences in gene expression. [89-90]

[79] Stephen M. Stack, David B. Brown & William C. Dewey, ³Visualization of interphase chromosomes,² Journal of Cell Science 26 (1977): 281299. Freely accessible (2011) at http://jcs.biologists.org/cgi/reprint/26/1/281

[80] Jenny A. Croft, Joanna M. Bridger, Shelagh Boyle, Paul Perry, Peter Teague & Wendy A. Bickmore, ³Differences in the Localization and Morphology of Chromosomes in the Human Nucleus,² Journal of Cell Biology 145 (1999): 11191131. Freely accessible (2011) at http://jcb.rupress.org/content/145/6/1119.full.pdf+html

[81] Heiner Albiez, Marion Cremer, Cinzia Tiberi, Lorella Vecchio, Lothar Schermelleh, Sandra Dittrich, Katrin Küpper, Boris Joffe, Tobias Thormeyer, Johann von Hase, Siwei Yang, Karl Rohr, Heinrich Leonhardt, Irina Solovei, Christoph Cremer, Stanislav Fakan & Thomas Cremer, ³Chromatin domains and the interchromatin compartment form structurally defined and functionally interacting nuclear networks,² Chromosome Research 14 (2006): 707733.

[82] Thomas Cremer & Marion Cremer, ³Chromosome Territories,² Cold Spring Harbor Perspectives in Biology 2 (2010): a003889. Freely accessible (2011) at http://cshperspectives.cshlp.org/content/2/3/a003889.full.pdf+html

[83] Emanuela V. Volpi, Edith Chevret, Tania Jones, Radost Vatcheva, Jill Williamson, Stephan Beck, R. Duncan Campbell, Michelle Goldsworthy, Stephen H. Powis, Jiannis Ragoussis, John Trowsdale & Denise Sheer, ³Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome chromosome 6 and its response to interferon in interphase nuclei,² Journal of Cell Science 113 (2000): 15651576. Freely accessible (2011) at http://jcs.biologists.org/cgi/reprint/113/9/1565

[84] Li-Feng Zhang, Khanh D. Huynh & Jeannie T. Lee, ³Perinucleolar
targeting of the inactive X during S phase: evidence for a role in the maintenance of silencing,² Cell 129 (2007): 693706.

[85] Christian Lanctôt, Thierry Cheutin, Marion Cremer, Giacomo Cavalli & Thomas Cremer, ³Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions,² Nature Reviews Genetics 8 (2007): 104115.

[86] Boris Joffe, Heinrich Leonhardt & Irina Solovei, ³Differentiation and large scale spatial organization of the genome,² Current Opinion in Genetics and Development 20 (2010): 562569.

[87] M. R. Hübner & D. L. Spector, ³Chromatin dynamics,² Annual Review of Biophysics 39 (2010): 471489.

[88] Hideki Tanizawa, Osamu Iwasaki, Atsunari Tanaka, Joseph R. Capizzi, Priyankara Wickramasinghe, Mihee Lee, Zhiyan Fu & Ken-ichi Noma, ³Mapping
of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation,² Nucleic Acids Research 38 (2010): 81648177. Freely accessible (2011) at http://nar.oxfordjournals.org/content/38/22/8164.long
[89] Luis A. Parada, Philip G. McQueen & Tom Misteli, ³Tissue-specific spatial organization of genomes,² Genome Biology 5:7 (2004): R44. Freely accessible (2011) at http://genomebiology.com/content/pdf/gb-2004-5-7-r44.pdf

[90] Tom Sexton, Heiko Schober, Peter Fraser & Susan M. Gasser, ³Gene regulation through nuclear organization,² Nature Structural & Molecular Biology 14 (2007): 10491055.

As to the 3-Dimensional structures of the cell communicating information. The cytoskeleton and microtubules have been implicated in quantum computation and communication. Though most work in this area has thus far been done on neuronal activity and consciousness, I believe that many details are relevant to unlocking many mysteries that have yet to be solved for the rest of molecular biology where 3-Dimensional organization is implicated in communicating overriding 'control' information downstream;
Electrodynamic Signaling by the Dendritic Cytoskeleton (Google Workshop on Quantum Biology) http://www.youtube.com/watch?v=0OO8E1_GJ4o Experimental Studies on a Single Microtubule (Google Workshop on Quantum Biology) http://www.youtube.com/watch?v=VQngptkPYE8
further note:
Coherence in the cytoskeleton http://www.quantum-mind.co.uk/coherence-in-the-cytoskeleton-c343.html
There was also this paper from Dr. Wells that came after he published 'The Myth of Junk DNA';
Gene Regulatory Networks in Embryos Depend on Pre-existing Spatial Coordinates - Jonathan Wells - July 2011 Excerpt: The development of metazoan embryos requires the precise spatial deployment of specific cellular functions. This deployment depends on gene regulatory networks (GRNs), which operate downstream of initial spatial inputs (E. H. Davidson, Nature 468 [2010]: 911). Those initial inputs depend, in turn, on pre-existing spatial coordinate systems. In Drosophila oocytes, for example, spatial localization of the earliest-acting elements of the maternal GRN depends on the prior establishment of an anteroposterior body axis by antecedent asymmetries in the ovary. Those asymmetries appear to depend on cytoskeletal and membrane patterns rather than on DNA sequences. I review that evidence, suggest that such patterns provide developmental information that must precede the operation of GRNs, and discuss possible implications of that information for evolutionary theory. http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=7751

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