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Genome Architecture: History
Please note this is an old version of this entry, which may differ significantly from the current revision.
Contributor: Yu Peng

Genome architecture is the multiscale spatial organization of genomic DNA and chromatin within the cell nucleus, encompassing the physical arrangement, folding, and interaction patterns through which chromosomes occupy three-dimensional nuclear space. In eukaryotic cells, this organization comprises nested structural levels that include nucleosome-associated chromatin, chromatin loops, topologically associating domains, larger chromatin compartments, and chromosome territories [1][2][3]. Genome architecture is characterized by non-random contact frequencies among genomic regions and by dynamic transitions in chromatin configuration that occur while the underlying DNA sequence remains spatially organized within the nucleus [1][2]. Architectural organization is generated and maintained through the physical properties of chromatin together with molecular processes involving structural proteins such as cohesin and CTCF, chromatin-associated factors, transcriptional machinery, and epigenetic states [2][3][4]. The concept therefore covers the three-dimensional topology, hierarchical folding, spatial positioning, interaction domains, and dynamic conformational organization of the genome as a chromatin-based molecular system [3][4].

  • 3D genome
  • chromatin organization
  • chromatin loops
  • topologically associating domains

🔵 Genomics and Chromatin Dynamics • 🟣 Molecular Biology • 🟡 Biochemistry, Genetics and Molecular Biology • 🔴 Life Sciences

References

  1. Erez Lieberman-Aiden; Nynke L. van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R. Lajoie; Peter J. Sabo; Michael O. Dorschner; et al. Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 2009, 326, 289-293, 10.1126/science.1181369.
  2. Jesse R. Dixon; Siddarth Selvaraj; Feng Yue; Audrey Kim; Yan Li; Yin Shen; Ming Hu; Jun S. Liu; Bing Ren; Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions. Nature 2012, 485, 376-380, 10.1038/nature11082.
  3. Ana Pombo; Niall Dillon; Three-dimensional Genome Architecture: Players and Mechanisms. Nat. Rev. Mol. Cell Biol. 2015, 16, 245-257, 10.1038/nrm3965.
  4. Ludvig Lizana; Yuri B. Schwartz; The Scales, Mechanisms, and Dynamics of the Genome Architecture. Sci. Adv. 2024, 10, eadm8167, 10.1126/sciadv.adm8167.
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