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Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations.

Iyer BV, Kenward M, Arya G - BMC Biophys (2011)

Bottom Line: Eukaryotic genomes possess an elaborate and dynamic higher-order structure within the limiting confines of the cell nucleus.Knowledge of the physical principles and the molecular machinery that govern the 3D organization of this structure and its regulation are key to understanding the relationship between genome structure and function.Here, we review results from these efforts and provide some additional insights that elucidate the relationship between structure and function at different hierarchical levels of genome organization.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0448, USA. garya@ucsd.edu.

ABSTRACT
Eukaryotic genomes possess an elaborate and dynamic higher-order structure within the limiting confines of the cell nucleus. Knowledge of the physical principles and the molecular machinery that govern the 3D organization of this structure and its regulation are key to understanding the relationship between genome structure and function. Elegant microscopy and chromosome conformation capture techniques supported by analysis based on polymer models are important steps in this direction. Here, we review results from these efforts and provide some additional insights that elucidate the relationship between structure and function at different hierarchical levels of genome organization.

No MeSH data available.


Illustration of the Genome Folding Problem. Illustration of the important question on genome organization. (Adapted with permission from cartoonist John Chase-http://www.chasetoons.com)
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Figure 1: Illustration of the Genome Folding Problem. Illustration of the important question on genome organization. (Adapted with permission from cartoonist John Chase-http://www.chasetoons.com)

Mentions: The DNA, thus packaged, occupies a significant portion of the nucleus volume while cellular factors that read, copy, modify, and maintain the genome, occupy the remaining. Ultimately, sophisticated patterns in cellular function arise due to a coupling between the accessibility of genetic information in the packaged DNA, and the organization and activity of cellular factors within the cell nucleus. For instance, nuclear processes like transcription, translation, repair and recombination do not occur ubiquitously in the nucleus, but are spatially compartmentalized in transcription, replication and recombination factories [1-3]. Clearly, how the 3D organization of the genome modulates these nuclear processes and how the nuclear processes in turn modify genome structure are important questions in modern cell biology. A critical step in addressing these questions requires a fundamental understanding of the genome 3D structure and the physical principles governing its organization, as articulated concisely yet powerfully in the cartoon of Figure 1.


Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations.

Iyer BV, Kenward M, Arya G - BMC Biophys (2011)

Illustration of the Genome Folding Problem. Illustration of the important question on genome organization. (Adapted with permission from cartoonist John Chase-http://www.chasetoons.com)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3102647&req=5

Figure 1: Illustration of the Genome Folding Problem. Illustration of the important question on genome organization. (Adapted with permission from cartoonist John Chase-http://www.chasetoons.com)
Mentions: The DNA, thus packaged, occupies a significant portion of the nucleus volume while cellular factors that read, copy, modify, and maintain the genome, occupy the remaining. Ultimately, sophisticated patterns in cellular function arise due to a coupling between the accessibility of genetic information in the packaged DNA, and the organization and activity of cellular factors within the cell nucleus. For instance, nuclear processes like transcription, translation, repair and recombination do not occur ubiquitously in the nucleus, but are spatially compartmentalized in transcription, replication and recombination factories [1-3]. Clearly, how the 3D organization of the genome modulates these nuclear processes and how the nuclear processes in turn modify genome structure are important questions in modern cell biology. A critical step in addressing these questions requires a fundamental understanding of the genome 3D structure and the physical principles governing its organization, as articulated concisely yet powerfully in the cartoon of Figure 1.

Bottom Line: Eukaryotic genomes possess an elaborate and dynamic higher-order structure within the limiting confines of the cell nucleus.Knowledge of the physical principles and the molecular machinery that govern the 3D organization of this structure and its regulation are key to understanding the relationship between genome structure and function.Here, we review results from these efforts and provide some additional insights that elucidate the relationship between structure and function at different hierarchical levels of genome organization.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0448, USA. garya@ucsd.edu.

ABSTRACT
Eukaryotic genomes possess an elaborate and dynamic higher-order structure within the limiting confines of the cell nucleus. Knowledge of the physical principles and the molecular machinery that govern the 3D organization of this structure and its regulation are key to understanding the relationship between genome structure and function. Elegant microscopy and chromosome conformation capture techniques supported by analysis based on polymer models are important steps in this direction. Here, we review results from these efforts and provide some additional insights that elucidate the relationship between structure and function at different hierarchical levels of genome organization.

No MeSH data available.