Abstract
Following fertilization in mammals, the chromatin landscape inherited from the two parental genomes and the nuclear organization are extensively reprogrammed. A tight regulation of nuclear organization is important for developmental success. One main nuclear feature is the organization of the chromosomes in discrete and individual nuclear spaces known as chromosome territories (CTs). In culture cells, their arrangements can be constrained depending on their genomic content (e.g., gene density or repeats) or by specific nuclear constrains such as the periphery or the nucleolus. However, during the early steps of mouse embryonic development, much less is known, specifically regarding how and when the two parental genomes intermingle. Here, we describe a three-dimensional fluorescence in situ hybridization (3D-FISH) for chromosome painting (3D-ChromoPaint) optimized to gain understanding in nuclear organization of specific CTs following fertilization. Our approach preserves the nuclear structure, and the acquired images allow full spatial analysis of interphase chromosome positioning and morphology across the cell cycle and during early development. This method will be useful in understanding the dynamics of chromosome repositioning during development as well as the alteration of chromosome territories upon changes in transcriptional status during key developmental steps. This protocol can be adapted to any other species or organoids in culture.
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References
Burton A, Torres-Padilla M-E (2010) Epigenetic reprogramming and development: a unique heterochromatin organization in the preimplantation mouse embryo. Brief Funct Genomics 9:444–454. https://doi.org/10.1093/bfgp/elq027
Borsos M, Torres-Padilla M-E (2016) Building up the nucleus: nuclear organization in the establishment of totipotency and pluripotency during mammalian development. Genes Dev 15:611–621. https://doi.org/10.1101/gad.273805.115
Zheng H, Huang B, Zhang B et al (2016) Resetting epigenetic memory by reprogramming of histone modifications in mammals. Mol Cell 63:1066–1079. https://doi.org/10.1016/j.molcel.2016.08.032
Probst AV, Almouzni G (2008) Pericentric heterochromatin: dynamic organization during early development in mammals. Differentiation 76:15–23. https://doi.org/10.1111/j.1432-0436.2007.00220.x
Borsos M, Perricone SM, Schauer T et al (2019) Genome–lamina interactions are established de novo in the early mouse embryo. Nature 569:729–733. https://doi.org/10.1038/s41586-019-1233-0
Martin C, Beaujean N, Brochard V et al (2006) Genome restructuring in mouse embryos during reprogramming and early development. Dev Biol 292:317–332. https://doi.org/10.1016/j.ydbio.2006.01.009
Aguirre-Lavin T, Adenot P, Bonnet-Garnier A et al (2012) 3D-FISH analysis of embryonic nuclei in mouse highlights several abrupt changes of nuclear organization during preimplantation development. BMC Dev Biol 12:30. https://doi.org/10.1186/1471-213X-12-30
Fulka H, Aoki F (2016) Nucleolus precursor bodies and ribosome biogenesis in early mammalian embryos: old theories and new discoveries. Biol Reprod 94(6):143. https://doi.org/10.1095/biolreprod.115.136093
Martin C, Brochard V, Carole M et al (2006) Architectural reorganization of the nuclei upon transfer into oocytes accompanies genome reprogramming. Mol Reprod Dev 73:1102–1111. https://doi.org/10.1002/mrd.20506
Burns KH, Viveiros MM, Ren Y et al (2003) Roles of NPM2 in chromatin and nucleolar organization in oocytes and embryos. Science 300:633–636. https://doi.org/10.1126/science.1081813
Cremer T, Cremer M (2010) Chromosome territories. Cold Spring Harb Perspect Biol 2:1–22. https://doi.org/10.1101/cshperspect.a003889
Lieberman-Aiden E, Van Berkum NL, Williams L et al (2009) Comprehensive mapping of long-range interactions reveals folding principles of the Human Genome. Science 326:289–294. https://doi.org/10.1126/science.1181369
Flyamer IM, Gassler J, Imakaev M et al (2017) Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature 544:110–114. https://doi.org/10.1038/nature21711
Du Z, Zheng H, Huang B et al (2017) Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nature 547:232–235. https://doi.org/10.1038/nature23263
Ke Y, Xu Y, Chen X et al (2017) 3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis. Cell 170:367–381.e20. https://doi.org/10.1016/j.cell.2017.06.029
Du Z, Zheng H, Kawamura Y et al (2020) Polycomb group proteins regulate chromatin architecture in mouse oocytes and early embryos article polycomb group proteins regulate chromatin architecture in mouse oocytes and early embryos. Mol Cell Biol 77:1–15. https://doi.org/10.1016/j.molcel.2019.11.011
Collombet S, Ranisavljevic N, Nagano T et al (2020) Parental-to-embryo switch of chromosome organization in early embryogenesis. Nature 580:142–146. https://doi.org/10.1038/s41586-020-2125-z
Galupa R, Heard E (2018) X-chromosome inactivation: a crossroads between chromosome architecture and gene regulation. Annu Rev Genet 52:535–566. https://doi.org/10.1146/annurev-genet-120116-024611
Croft JA, Bridger JM, Boyle S et al (1999) Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol 145:1119–1131. https://doi.org/10.1083/jcb.145.6.1119
Koehler D, Zakhartchenko V, Froenicke L et al (2009) Changes of higher order chromatin arrangements during major genome activation in bovine preimplantation embryos. Exp Cell Res 315:2053–2063. https://doi.org/10.1016/j.yexcr.2009.02.016
Heride C, Ricoul M, Kiêu K et al (2010) Distance between homologous chromosomes results from chromosome positioning constraints. J Cell Sci 123:4063–4075. https://doi.org/10.1242/jcs.066498
Zhang LF, Huynh KD, Lee JT (2007) Perinucleolar targeting of the inactive X during S phase: evidence for a role in the maintenance of silencing. Cell 129:693–706. https://doi.org/10.1016/j.cell.2007.03.036
Namekawa SH, Payer B, Huynh KD et al (2010) Two-step imprinted X inactivation: repeat versus genic silencing in the mouse. Mol Cell Biol 30:3187–3205. https://doi.org/10.1128/mcb.00227-10
Ranisavljevic N, Okamoto I, Heard E, Ancelin K (2017) RNA FISH to study zygotic genome activation in early mouse embryos. Methods Mol Biol 1605:133–145. https://doi.org/10.1007/978-1-4939-6988-3_9
Hogan B, Beddington R, Costantini F, Facy E (1994) Manipulating the mouse embryo. Cold Sring Harbor Laboratory Press, New York
Acknowledgments
We thank the Institut Curie animal facility for animal welfare and husbandry and the imaging facility PICT-IBiSA@BDD (member of France-Bioimaging ANR-10-INBS-04 and UMR3215/U934) for technical assistance. This work was supported by ANR-09-Blanc-0114 to METP and EH and Labex DEEP:ANR-11-LBX-0044, IDEX PSL: ANR-10-IDEX-0001-02 PSL to E.H.
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Ancelin, K., Miyanari, Y., Leroy, O., Torres-Padilla, ME., Heard, E. (2021). Mapping of Chromosome Territories by 3D-Chromosome Painting During Early Mouse Development. In: Ancelin, K., Borensztein, M. (eds) Epigenetic Reprogramming During Mouse Embryogenesis. Methods in Molecular Biology, vol 2214. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0958-3_12
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DOI: https://doi.org/10.1007/978-1-0716-0958-3_12
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