Three-Dimensional Simulation of Whole-Genome Structuring Through the Transition from Anaphase to Interphase.

Item request has been placed! ×
Item request cannot be made. ×
loading   Processing Request
Read More Add to Saved list
  • Additional Information
    • Source:
      Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE
    • Publication Information:
      Publication: Totowa, NJ : Humana Press
      Original Publication: Clifton, N.J. : Humana Press,
    • Subject Terms:
      Anaphase*/genetics ; Interphase*/genetics ; Genome, Human* ; Chromatin*/genetics ; Chromatin*/metabolism; Humans ; Computer Simulation ; Chromosomes, Human/genetics ; Mitosis/genetics
    • Abstract:
      In order to analyze the three-dimensional genome architecture, it is important to simulate how the genome is structured through the cell cycle progression. In this chapter, we present the usage of our computation codes for simulating how the human genome is formed as the cell transforms from anaphase to interphase. We do not use the global Hi-C data as an input into the genome simulation but represent all chromosomes as linear polymers annotated by the neighboring region contact index (NCI), which classifies the A/B type of each local chromatin region. The simulated mitotic chromosomes heterogeneously expand upon entry to the G1 phase, which induces phase separation of A and B chromatin regions, establishing chromosome territories, compartments, and lamina and nucleolus associations in the interphase nucleus. When the appropriate one-dimensional chromosomal annotation is possible, using the protocol of this chapter, one can quantitatively simulate the three-dimensional genome structure and dynamics of human cells of interest.
      (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
    • References:
      Walter J, Schermelleh L, Cremer M, Tashiro S, Cremer T (2003) Chromosome order in HeLa cells changes during mitosis and early G1, but is stably maintained during subsequent interphase stages. J Cell Biol 160:685–697. (PMID: 10.1083/jcb.200211103126045932173351)
      Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J (2013) Organization of the mitotic chromosome. Science 342:948–953. (PMID: 10.1126/science.1236083242008124040465)
      Larson AG, Elnatan D, Keenen MM et al (2017) Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature 547:236–240. (PMID: 10.1038/nature22822286366045606208)
      Boija A, Klein IA, Sabari BR et al (2018) Transcription factors activate genes through the phase-separation capacity of their activation domains. Cell 175:1842–1855.e16. (PMID: 10.1016/j.cell.2018.10.04230449618)
      MacPherson Q, Beltran B, Spakowitz AJ (2018) Bottom-up modeling of chromatin segregation due to epigenetic modifications. Proc Natl Acad Sci USA 115:12739–12744. (PMID: 10.1073/pnas.1812268115304780426294944)
      Krakoviack V, Hansen J-P, Louis AA (2003) Influence of solvent quality on effective pair potentials between polymers in solution. Phys Rev E 67:041801. (PMID: 10.1103/PhysRevE.67.041801)
      Fujishiro S, Sasai M (2022) Generation of dynamic three-dimensional genome structure through phase separation of chromatin. Proc Natl Acad Sci USA 119:e2109838119. (PMID: 10.1073/pnas.2109838119356174339295772)
      Rao SS, Huntley MH, Durand NC et al (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159:1665–1680. (PMID: 10.1016/j.cell.2014.11.021254975475635824)
      Stukowski A (2010) Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool. Modelling Simul Mater Sci Eng 18:015012. (PMID: 10.1088/0965-0393/18/1/015012)
      Németh A, Längst G (2011) Genome organization in and around the nucleolus. Trends Genet 27:149–156. (PMID: 10.1016/j.tig.2011.01.00221295884)
      Lazaris C et al (2017) HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking. BMC Genom 18:22.
      Bersaglieri C, Santoro R (2023) Methods for mapping 3D-chromosome architecture around nucleoli. Curr Opin Cell Biol 81:102171.
    • Contributed Indexing:
      Keywords: Cell cycle; Genome organization; Phase separation; Simulation
    • Accession Number:
      0 (Chromatin)
    • Publication Date:
      Date Created: 20240916 Date Completed: 20240916 Latest Revision: 20240916
    • Publication Date:
      20240917
    • Accession Number:
      10.1007/978-1-0716-4136-1_18
    • Accession Number:
      39283460