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Molecular mapping of nuclear organization in the mouse preimplantation embryo
Molecular mapping of nuclear organization in the mouse preimplantation embryo
Upon fertilization the two parental genomes are extensively reprogrammed to give rise to a totipotent state. In the mammalian embryo, this epigenetic reprogramming involves an extensive three dimensional (3D) rearrangement of nuclear organization which only recently have been started to be investigated on a genome-wide scale. The positioning of loci relative to the nuclear periphery has been shown to change during differentiation, potentially regulating gene expression and chromatin. Therefore, it is of question whether the nuclear reorganization in early embryonic cells correlates with or even regulates genome function and embryo development. During my PhD work, we have created maps of lamina associated domains (LADs) from mouse preimplantation embryos and oocytes at the single cell level. LADs are genomic regions that reside at the nuclear periphery and represent a lowly transcribed, gene-poor fraction of the genome originally identified in somatic cells. We have found that LADs are absent in oocytes but become established already in zygotes and are dynamically rearranged during the 2- and 8-cell stages with little heterogeneity between individual cells. We obtained LAD data from hybrid embryos to distinguish the parental genomes by single nucleotide polymorphisms (SNPs) in sequencing. Our analysis unravelled differences in genome organization between the two parental alleles that likely reflect their different germline history. Moreover, we find that LAD formation precedes the maturation of topologically associated domains (TADs) in a DNA replication independent manner. Additionally, we observed that only the X chromosome contacts the lamina in oocytes, potentially through an interaction with the Lamin B Receptor (LBR) protein. Eventually, we identified an epigenetic asymmetry of H3K4 methylation on LADs between the paternal and maternal genomes in zygotes. We found that the experimental reduction of the H3K4me3 histone mark by the overexpression of the lysine demethylase Kdm5b results in a loss of LAD structure, specifically in the paternal zygotic genome. In conclusion, we have uncovered a novel mechanism of allele specific LAD formation through histone methylation. Additionally, this work provides genome wide information on mouse preimplantation nuclear organization contributing a resource for further epigenetic studies of early embryos.
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Borsos, Máté
2018
English
Universitätsbibliothek der Ludwig-Maximilians-Universität München
Borsos, Máté (2018): Molecular mapping of nuclear organization in the mouse preimplantation embryo. Dissertation, LMU München: Faculty of Biology
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Abstract

Upon fertilization the two parental genomes are extensively reprogrammed to give rise to a totipotent state. In the mammalian embryo, this epigenetic reprogramming involves an extensive three dimensional (3D) rearrangement of nuclear organization which only recently have been started to be investigated on a genome-wide scale. The positioning of loci relative to the nuclear periphery has been shown to change during differentiation, potentially regulating gene expression and chromatin. Therefore, it is of question whether the nuclear reorganization in early embryonic cells correlates with or even regulates genome function and embryo development. During my PhD work, we have created maps of lamina associated domains (LADs) from mouse preimplantation embryos and oocytes at the single cell level. LADs are genomic regions that reside at the nuclear periphery and represent a lowly transcribed, gene-poor fraction of the genome originally identified in somatic cells. We have found that LADs are absent in oocytes but become established already in zygotes and are dynamically rearranged during the 2- and 8-cell stages with little heterogeneity between individual cells. We obtained LAD data from hybrid embryos to distinguish the parental genomes by single nucleotide polymorphisms (SNPs) in sequencing. Our analysis unravelled differences in genome organization between the two parental alleles that likely reflect their different germline history. Moreover, we find that LAD formation precedes the maturation of topologically associated domains (TADs) in a DNA replication independent manner. Additionally, we observed that only the X chromosome contacts the lamina in oocytes, potentially through an interaction with the Lamin B Receptor (LBR) protein. Eventually, we identified an epigenetic asymmetry of H3K4 methylation on LADs between the paternal and maternal genomes in zygotes. We found that the experimental reduction of the H3K4me3 histone mark by the overexpression of the lysine demethylase Kdm5b results in a loss of LAD structure, specifically in the paternal zygotic genome. In conclusion, we have uncovered a novel mechanism of allele specific LAD formation through histone methylation. Additionally, this work provides genome wide information on mouse preimplantation nuclear organization contributing a resource for further epigenetic studies of early embryos.