Loss of totipotentcy in an early embryo is directed by molecular processes responsible for cell fate decisions. Three dimensional genome organisation is an important factor linking chromatin architecture with stage specific gene expression patterns. Little is known about the role of chromosome organisation in gene expression regulation of lineage specific factors in mammalian embryos. Using bovine embryos as a model we have described these interactions at key developmental stages. Three bovine chromosomes (BTA) that differ in size, number of carried genes, and contain loci for key lineage regulators OCT4, NANOG and CDX2, were investigated. The results suggest that large chromosomes regardless of their gene density (BTA12 gene-poor, BTA5 gene-rich) do not significantly change their radial position within the nucleus. Gene loci however, may change its position within the chromosome territory (CT) and relocate its periphery, when stage specific process of gene activation is required. Trophectoderm specific CDX2 and epiblast precursor NANOG loci tend to locate on the surface or outside of the CTs, at stages related with their high expression. We postulate that the observed changes in CT shape reflect global alternations in gene expression related to differentiation.

Department of Genetics and Animal Breeding Poznan University of Life Sciences Poznan Poland

Veterinary Research Institute Brno Czech Republic

See more in PubMed

Borsos M, Torres-Padilla ME. Building up the nucleus: nuclear organization in the establishment of totipotency and pluripotency during mammalian development. Genes & development. 2016;30(6):611–21. doi: 10.1101/gad.273805.115 ; PubMed DOI PMC

Koehler D, Zakhartchenko V, Froenicke L, Stone G, Stanyon R, Wolf E, et al. Changes of higher order chromatin arrangements during major genome activation in bovine preimplantation embryos. Experimental cell research. 2009;315(12):2053–63. doi: 10.1016/j.yexcr.2009.02.016 . PubMed DOI

Meister P, Mango SE, Gasser SM. Locking the genome: nuclear organization and cell fate. Current opinion in genetics & development. 2011;21(2):167–74. doi: 10.1016/j.gde.2011.01.023 ; PubMed DOI PMC

Talamas JA, Capelson M. Nuclear envelope and genome interactions in cell fate. Frontiers in genetics. 2015;6:95 doi: 10.3389/fgene.2015.00095 ; PubMed DOI PMC

Tarkowski AK, Wróblewska J. Development of blastomeres of mouse eggs isolated at the 4- and 8-cell stage. J Embriol exp Morph. 1967;18(1):155–80. PubMed

Johnson MH, Ziomek CA. The foundation of two distinct cell lineages within the mouse morula. Cell. 1981;24(1):71–80. PubMed

Maitre JL, Turlier H, Illukkumbura R, Eismann B, Niwayama R, Nedelec F, et al. Asymmetric division of contractile domains couples cell positioning and fate specification. Nature. 2016;536(7616):344–8. doi: 10.1038/nature18958 ; PubMed DOI PMC

Latos PA, Sienerth AR, Murray A, Senner CE, Muto M, Ikawa M, et al. Elf5-centered transcription factor hub controls trophoblast stem cell self-renewal and differentiation through stoichiometry-sensitive shifts in target gene networks. Genes Dev. 2015;29(23):2435–48. doi: 10.1101/gad.268821.115 ; PubMed DOI PMC

Ng RK, Dean W, Dawson C, Lucifero D, Madeja Z, Reik W, et al. Epigenetic restriction of embryonic cell lineage fate by methylation of Elf5. Nature Cell Biology. 2008;10(11):1280–U68. doi: 10.1038/ncb1786 PubMed DOI PMC

Niwa H, Toyooka Y, Shimosato D, Strumpf D, Takahashi K, Yagi R, et al. Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation. Cell. 2005;123(5):917–29. doi: 10.1016/j.cell.2005.08.040 . PubMed DOI

Strumpf D, Mao CA, Yamanaka Y, Ralston A, Chawengsaksophak K, Beck F, et al. Cdx2 is required for correct cell fate specification and differentiation of trophectoderm in the mouse blastocyst. Development. 2005;132(9):2093–102. doi: 10.1242/dev.01801 . PubMed DOI

Saiz N, Plusa B. Early cell fate decisions in the mouse embryo. Reproduction. 2013;145(3):R65–80.: doi: 10.1530/REP-12-0381 . PubMed DOI

Niwa H, Miyazaki J-i, Smith AG. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nature genetics. 2000;24(4):372–6. http://www.nature.com/ng/journal/v24/n4/suppinfo/ng0400_372_S1.html doi: 10.1038/74199 PubMed DOI

Chambers I, Colby D, Robertson M, Nichols J, Lee S, Tweedie S, et al. Functional Expression Cloning of Nanog, a Pluripotency Sustaining Factor in Embryonic Stem Cells. Cell. 2003;113:643–55. PubMed

Mitsui K, Tokuzawa Y, Itoh H, Segawa K, Murakami M, Maeda M, et al. The Homeoprotein Nanog Is Required for Maintenance of Pluripotency in Mouse Epiblast and ES Cells. Cell. 2003;113:631–42. PubMed

Mak W, Nesterova TB, de Napoles M, Appanah R, Yamanaka S, Otte AP, et al. Reactivation of the Paternal X Chromosome in Early Mouse Embryos. Science. 2004;303(5658):666–9.: doi: 10.1126/science.1092674 PubMed DOI

Okamoto I, Otte AP, Allis CD, Reinberg D, Heard E. Epigenetic Dynamics of Imprinted X Inactivation During Early Mouse Development. Science. 2004;303(5658):644–9.: doi: 10.1126/science.1092727 PubMed DOI

Silva SS, Rowntree RK, Mekhoubad S, Lee JT. X-chromosome inactivation and epigenetic fluidity in human embryonic stem cells. Proc Natl Acad Sci U S A. 2008;105(12):4820–5. doi: 10.1073/pnas.0712136105 ; PubMed DOI PMC

Madeja ZE, Sosnowski J, Hryniewicz K, Warzych E, Pawlak P, Rozwadowska N, et al. Changes in sub-cellular localisation of trophoblast and inner cell mass specific transcription factors during bovine preimplantation development. Bmc Developmental Biology. 2013;13 doi: 10.1186/1471-213x-13-32 PubMed DOI PMC

Kuijk EW, Puy LD, Tol HTAV, Oei CHY, Haagsman HP, Colenbrander B, et al. Differences in early lineage segregation between mammals. Developmental Dynamics. 2008;237(4):918–27. doi: 10.1002/dvdy.21480 PubMed DOI

Kuijk EW, van Tol LT, Van de Velde H, Wubbolts R, Welling M, Geijsen N, et al. The roles of FGF and MAP kinase signaling in the segregation of the epiblast and hypoblast cell lineages in bovine and human embryos. Development. 2012;139(5):871–82. doi: 10.1242/dev.071688 ; PubMed DOI PMC

Caufmann G, Van de Velde H, Liebaers I, Van Steirteghen A. Oct-4 mRNA and protein expression during human preimplantation development. Molecular human reproduction. 2005;11:173–81. doi: 10.1093/molehr/gah155 PubMed DOI

Guest DJ, Allen WR. Expression of Cell-Surface Antigens and Embryonic Stem Cell Pluripotency Genes in Equine Blastocysts Stem cells and development. 2007;16:789–96. doi: 10.1089/scd.2007.0032 PubMed DOI

Kobolak J, Kiss K, Polgar Z, Mamo S, Rogel-Gaillard C, Tancos Z, et al. Promoter analysis of the rabbit POU5F1 gene and its expression in preimplantation stage embryos. BMC Mol Biol. 2009;10:88 doi: 10.1186/1471-2199-10-88 ; PubMed DOI PMC

Sritanaudomchai H, Sparman M, Tachibana M, Clepper L, Woodward J, Gokhale S, et al. CDX2 in the formation of the trophectoderm lineage in primate embryos. Developmental biology. 2009;335(1):179–87. doi: 10.1016/j.ydbio.2009.08.025 ; PubMed DOI PMC

Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature reviews Genetics. 2001;2(4):292–301. doi: 10.1038/35066075 . PubMed DOI

Albiez H, Cremer M, Tiberi C, Vecchio L, Schermelleh L, Dittrich S, et al. Chromatin domains and the interchromatin compartment form structurally defined and functionally interacting nuclear networks. Chromosome research: an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology. 2006;14(7):707–33. doi: 10.1007/s10577-006-1086-x . PubMed DOI

Di Stefano M, Paulsen J, Lien TG, Hovig E, Micheletti C. Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization. Scientific reports. 2016;6:35985 doi: 10.1038/srep35985 ; PubMed DOI PMC

Ragoczy T, Telling A, Sawado T, Groudine M, Steven T.Kosa ST. A genetic analysis of chromosome territory looping: diverse roles for distal regulatory elements. Chromosome research: an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology. 2003;11(5). PubMed

Deng W, Rupon JW, Krivega I, Breda L, Motta I, Jahn KS, et al. Reactivation of developmentally silenced globin genes by forced chromatin looping. Cell. 2014;158(4):849–60. doi: 10.1016/j.cell.2014.05.050 ; PubMed DOI PMC

Ahmed K, Dehghani H, Rugg-Gunn P, Fussner E, Rossant J, Bazett-Jones DP. Global chromatin architecture reflects pluripotency and lineage commitment in the early mouse embryo. PloS one. 2010;5(5):e10531 doi: 10.1371/journal.pone.0010531 ; PubMed DOI PMC

Efroni S, Duttagupta R, Cheng J, Dehghani H, Hoeppner DJ, Dash C, et al. Global transcription in pluripotent embryonic stem. Cell stem cell. 2008;2(5):437–47.: doi: 10.1016/j.stem.2008.03.021 ; PubMed DOI PMC

Meshorer E, Misteli T. Chromatin in pluripotent embryonic stem cells and differentiation. Nature Reviews Molecular Biology. 2006;7:540–6. PubMed

Van Soom A, Ysebaert MT, De Kruif A. Relationship Between Timing of Development, Morula Morphology, and Cell Allocation to Inner Cell Mass and Trophectoderm in In Vitro-Produced Bovine Embryos. Molecular reproduction and development. 1997;47:47–56. doi: 10.1002/(SICI)1098-2795(199705)47:1<47::AID-MRD7>3.0.CO;2-Q PubMed DOI

Iannuccelli E, Mompart F, Gellin J, Lahbib-Mansais Y, Yerle M, Boudier T. NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments. Bioinformatics. 2010;26(5):696–7.: doi: 10.1093/bioinformatics/btq013 . PubMed DOI

Kociucka B, Cieslak J, Szczerbal I. Three-dimensional arrangement of genes involved in lipid metabolism in nuclei of porcine adipocytes and fibroblasts in relation to their transcription level. Cytogenetic and genome research. 2012;136(4):295–302. doi: 10.1159/000338255 . PubMed DOI

Sehgal N, Fritz AJ, Morris K, Torres I, Chen Z, Xu J, et al. Gene density and chromosome territory shape. Chromosoma. 2014;123(5):499–513. doi: 10.1007/s00412-014-0480-y PubMed DOI PMC

Goossens K, Van Soom A, Van Poucke M, Vandaele L, Vandesompele J, Van Zeveren A, et al. Identification and expression analysis of genes associated with bovine blastocyst formation. BMC developmental biology. 2007;7:64 doi: 10.1186/1471-213X-7-64 ; PubMed DOI PMC

Khan DR, Dube D, Gall L, Peynot N, Ruffini S, Laffont L, et al. Expression of pluripotency master regulators during two key developmental transitions: EGA and early lineage specification in the bovine embryo. PloS one. 2012;7(3):e34110 doi: 10.1371/journal.pone.0034110 ; PubMed DOI PMC

Goossens K, Van Poucke M, Van Soom A, Vandesompele J, Van Zeveren A, Peelman LJ. Selection of reference genes for quantitative real-time PCR in bovine preimplantation embryos. BMC developmental biology. 2005;5:27 doi: 10.1186/1471-213X-5-27 ; PubMed DOI PMC

Li L, Zheng P, Dean J. Maternal control of early mouse development. Development. 2010;137(6):859–70. doi: 10.1242/dev.039487 ; PubMed DOI PMC

Zuccotti M, Merico V, Belli M, Mulas F, Sacchi L, Zupan B, et al. OCT4 and the acquisition of oocyte developmental competence during folliculogenesis. The International journal of developmental biology. 2012;56(10–12):853–8. doi: 10.1387/ijdb.120174mz . PubMed DOI

Bonev B, Cavalli G. Organization and function of the 3D genome. Nature reviews Genetics. 2016;17(11):661–78. doi: 10.1038/nrg.2016.112 PubMed DOI

Zeng F, Schultz RM. RNA transcript profiling during zygotic gene activation in the preimplantation mouse embryo. Developmental biology. 2005;283(1):40–57. doi: 10.1016/j.ydbio.2005.03.038 . PubMed DOI

Mamo S, Rizos D, Lonergan P. Transcriptomic changes in the bovine conceptus between the blastocyst stage and initiation of implantation. Animal Reproduction Science. 2012;134(1):56–63. doi: 10.1016/j.anireprosci.2012.08.011 PubMed DOI

Memili F, First NL. Control of gene expression at the onset of bovine embryonic developmen. Biology of Reproduction. 1999;61:1198–207. PubMed

Plusa B, Piliszek A, Frankenberg S, Artus J, Hadjantonakis AK. Distinct sequential cell behaviours direct primitive endoderm formation in the mouse blastocyst. Development. 2008;135(18):3081–91. doi: 10.1242/dev.021519 ; PubMed DOI PMC

Artus J, Hadjantonakis AK. Troika of the Mouse Blastocyst: Lineage Segregation and Stem Cells. Current Stem Cell Research Theories. 2012;7(1):78–91. PubMed PMC

Yuzyuk T, Fakhouri TH, Kiefer J, Mango SE. The polycomb complex protein mes-2/E(z) promotes the transition from developmental plasticity to differentiation in C. elegans embryos. Developmental cell. 2009;16(5):699–710. doi: 10.1016/j.devcel.2009.03.008 ; PubMed DOI PMC

Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell. 2010;38(4):603–13. doi: 10.1016/j.molcel.2010.03.016 . PubMed DOI PMC

Wu X, Song M, Yang X, Liu X, Liu K, Jiao C, et al. Establishment of bovine embryonic stem cells after knockdown of CDX2. Scientific reports. 2016;6:28343 doi: 10.1038/srep28343 ; PubMed DOI PMC

Wiblin AE, Cui W, Clark AJ, Bickmore WA. Distinctive nuclear organisation of centromeres and regions involved in pluripotency in human embryonic stem cells. Journal of Cell Science. 2005;118. PubMed

Berg DK, Smith CS, Pearton DJ, Wells DN, Broadhurst R, Donnison M, et al. Trophectoderm lineage determination in cattle. Developmental cell. 2011;20(2):244–55. doi: 10.1016/j.devcel.2011.01.003 . PubMed DOI

Madeja ZE, Hryniewicz K, Orsztynowicz M, Pawlak P, Perkowska A. WNT/β-catenin signalling affects cell lineage and pluripotency specific gene expression in bovine blastocysts–prospects for bovine ESC derivation. Stem Cells and Development. 2015;24:2437–54. doi: 10.1089/scd.2015.0053 PubMed DOI

Bou G, Liu S., Guo J, Zhao Y, Sun M, Xue B, et al. Cdx2 represses Oct4 function via inducing its proteasome-dependent degradation in early porcine embryos. Developmental biology. 2016;410(1):36–44. doi: 10.1016/j.ydbio.2015.12.014 PubMed DOI

Goetze S, Mateos-Langerak J, van Driel R. Three-dimensional genome organization in interphase and its relation to genome function. Seminars in Cell & Developmental Biology. 2007;18(5):707–14. http://dx.doi.org/10.1016/j.semcdb.2007.08.007. PubMed DOI

Eils R, Dietzel S, Bertin E, Schrock E, Speicher MR, Ried T, et al. Three-dimensional Reconstruction of Painted Human Interphase Chromosomes: Active and Inactive X Chromosome Territories Have Similar Volumes but Differ in Shape and Surface Structure J Cell Biol. 1996;135(1):1427–40. PubMed PMC

Graf A, Krebs S, Zakhartchenko V, Schwalb B, Blum H, Wolf E. Fine mapping of genome activation in bovine embryos by RNA sequencing. Proc Natl Acad Sci U S A. 2014;111(11):4139–44. doi: 10.1073/pnas.1321569111 ; PubMed DOI PMC