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Related Concept Videos

Crossing Over01:30

Crossing Over

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Crossing over is the exchange of genetic information between homologous chromosomes during prophase I of meiosis I. Genetic recombination gives rise to allelic diversity in the newly formed daughter cells. In humans, crossing over produces genetically distinct haploid egg and sperm cells that undergo fertilization to produce unique offspring. Before cell division starts, the germ cell’s chromosome(s) undergo duplication in the S phase of the cell cycle. As the cells enter prophase I,...
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Unlike mitosis, meiosis aims for genetic diversity in its creation of haploid gametes. Dividing germ cells first begin this process in prophase I, where each chromosome—replicated in S phase—is now composed of two sister chromatids (identical copies) joined centrally.
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A functional eukaryotic chromosome must contain three elements: a centromere, telomeres, and numerous origins of replication.
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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Before a cell can divide, it must accurately replicate all of its chromosomes, including the DNA and its associated histone and non-histone proteins.  This process begins at numerous origins of replication during the S phase of the cell cycle in each of a cell’s chromosomes simultaneously. Certain nucleotides can act as origins of replication, but these sequences are not well defined - especially in complex, multi-cellular, eukaryotic species. The length of DNA that spans an origin...
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Related Experiment Video

Updated: Feb 28, 2026

Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization
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Recurrence plot reconstruction reveals chromosomal reorganization before territory formation.

Yuki Kitanishi1,2, Hiroki Sugishita1,2, Yukiko Gotoh1,2

  • 1Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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Summary

The recurrence plot-based reconstruction (RPR) method successfully analyzed single-cell Hi-C data from early embryos. This revealed dynamic 3D genome reorganization and chromosome territory formation during early development.

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Area of Science:

  • Genomics
  • Developmental Biology
  • Cell Biology

Background:

  • Chromatin conformation capture (Hi-C) methods advance nuclear architecture understanding.
  • Reconstructing 3D genome structure from low-contact single-cell Hi-C (scHi-C) data is challenging.

Purpose of the Study:

  • To apply the recurrence plot-based reconstruction (RPR) method to scHi-C data for analyzing early embryonic 3D genome organization.
  • To investigate dynamic chromosomal reorganization and territory formation during early embryogenesis.

Main Methods:

  • Utilized the recurrence plot-based reconstruction (RPR) method.
  • Analyzed single-cell Hi-C (scHi-C) data from early-stage F1 hybrid embryos.

Main Results:

  • Paternal and maternal chromosomes gradually intermingled from 1-cell to 64-cell stages.
  • Discrete chromosome territories were established between the 8-cell and 64-cell stages.
  • Observed Rabl-like polarization, transient rod-like extension, and parallel chromosome alignment, indicating dynamic reorganization before territory formation.

Conclusions:

  • The RPR method effectively reconstructs 3D genome architecture from scHi-C data.
  • scHi-C combined with RPR captures dynamic 3D chromosomal architecture during early embryogenesis.
  • Early embryogenesis involves significant chromosomal reorganization prior to the establishment of distinct territories.