Three-dimensional organization
of a self-replicating nano-fabrication site:
the human cell nucleus
Division
Biophysics of Macromolecules, German Cancer Research
Centre
This is an abstract
for a poster to be presented at the
Fifth
Foresight Conference on Molecular Nanotechnology.
There will be a link from here to the full article when it is
available on the web.
The eukaryotic cell is a prime example of a functioning
nano-machinery. The synthesis of proteins, maintenance of
structure and duplication of the machinery itself are all
fine-tuned biochemical processes that depend on the precise
structural arrangement of the cellular components. Especially the
regulation of genes has been shown to be connected closely to the
organization of the genome in the nucleus.
The nucleus of the cell has for a long time been viewed as a
'spaghetti soup' of DNA bound to various proteins without much
internal structure, except during cell division when chromosomes
are condensed into separate entities. Only recently has it become
apparent that chromosomes occupy distinct 'territories' also in
the interphase, i.e. between cell divisions. In an analogy of the
Bauhaus principle that "form follows function" we
believe that analyzing in which form DNA is organized in these
territories will help us to understand genomic function. We use
computer models - Monte Carlo and Brownian dynamics simulations -
to develop plausible proposals for the structure of the
interphase genome and compare them to experimental data. In the
work presented here, we simulate interphase chromosomes for
different folding morphologies of the chromatin fiber which is
organized into loops of 100 kbp to 3 Mbp that can be
interconnected in various ways. The backbone of the fiber is
described by a wormlike-chain polymer whose diameter and
stiffness can be estimated from independent measurements. The
implementation describes this polymer as a segmented chain with
3000 to 20000 segments for chromosome 15 depending on the phase
of the simulation. The modeling is performed on a parallel
computer (IBM SP2 with 80 nodes). Currently we determine genomic
marker distributions within the Prader-Willi-Region on chromosome
15q11.2-13.3. For these measurements we use a fluorescence in
situ hybridisation method (in collaboration with I. Solovai, J.
Crai and T. Cremer, Munich, FRG) conserving the structure of the
nucleus. As probes we use 10 kbp long lambda clones (Prof. B.
Horsthemke, Essen, FRG) covering genomic marker distances between
8 kbp and 250 kbp. The markers are detected with confocal and
standing wavefield light microscopes (in collaboration with
J.Rauch, J. Bradl, C. Cremer and E.Stelzer, both Heidelberg, FRG)
and using special image reconstruction methods developed solely
for this purpose (developed by R. Eils. and W. Jaeger,
Heidelberg, FRG).
The work is part of the Heidelberg 3D Human Genome Study
Group, which is part of the German Human Genome Project.
*Corresponding Address:
Tobias A. Knoch, Division Biophysics of Macromolecules, German
Cancer Research Centre, Im Neuenheimer Feld 280, D - 69120
Heidelberg, Germany, ph: +49-6221/423394 or 423392 fax:
+49-6221/422291 email: [email protected]
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