scholarly journals Genome-wide decoupling of H2Aub and H3K27me3 in early mouse development

2021 ◽  
Author(s):  
Yezhang Zhu ◽  
Jiali Yu ◽  
Yan Rong ◽  
Yun-Wen Wu ◽  
Heng-Yu Fan ◽  
...  
Keyword(s):  
Polycomb Group ◽  
Mammalian Development ◽  
Mouse Development ◽  
Chromatin Regulators ◽  
Genome Wide ◽  
A Genome ◽  
Independent Functions ◽  
Preimplantation Mouse ◽  
Early Mouse ◽  
Early Mammalian Development

Polycomb group (PcG) proteins are crucial chromatin regulators during development. H2Aub and H3K27me3 are catalyzed by Polycomb-repressive Complex 1 and 2 (PRC1/2) respectively, and largely overlap in the genome due to mutual recruitment of the two complexes. However, whether PRC1/H2Aub and PRC2/H3K27me3 can function independently remains obscure. Here we uncovered a genome-wide decoupling of H2Aub and H3K27me3 in preimplantation mouse embryos, at both canonical PcG targets and broad distal domains. H2Aub represses future bivalent genes without H3K27me3 but does not contribute to maintenance of H3K27me3-dependent non-canonical imprinting. Our study thus revealed their distinct and independent functions in early mammalian development.

scholarly journals Dnmt1 binds and represses genomic retroelements via DNA methylation in mouse early embryos

2020 ◽  
Vol 48 (15) ◽  
pp. 8431-8444 ◽  
Author(s):  
Byungkuk Min ◽  
Jung Sun Park ◽  
Young Sun Jeong ◽  
Kyuheum Jeon ◽  
Yong-Kook Kang
Keyword(s):  
Dna Methylation ◽  
Cpg Islands ◽  
Endogenous Retrovirus ◽  
Dna Demethylation ◽  
Mouse Development ◽  
Genome Wide ◽  
Early Embryos ◽  
Dna Adenine Methylase ◽  
Early Mouse ◽  
Early Developmental

Abstract Genome-wide passive DNA demethylation in cleavage-stage mouse embryos is related to the cytoplasmic localization of the maintenance methyltransferase DNMT1. However, recent studies provided evidences of the nuclear localization of DNMT1 and its contribution to the maintenance of methylation levels of imprinted regions and other genomic loci in early embryos. Using the DNA adenine methylase identification method, we identified Dnmt1-binding regions in four- and eight-cell embryos. The unbiased distribution of Dnmt1 peaks in the genic regions (promoters and CpG islands) as well as the absence of a correlation between the Dnmt1 peaks and the expression levels of the peak-associated genes refutes the active participation of Dnmt1 in the transcriptional regulation of genes in the early developmental period. Instead, Dnmt1 was found to associate with genomic retroelements in a greatly biased fashion, particularly with the LINE1 (long interspersed nuclear elements) and ERVK (endogenous retrovirus type K) sequences. Transcriptomic analysis revealed that the transcripts of the Dnmt1-enriched retroelements were overrepresented in Dnmt1 knockdown embryos. Finally, methyl-CpG-binding domain sequencing proved that the Dnmt1-enriched retroelements, which were densely methylated in wild-type embryos, became demethylated in the Dnmt1-depleted embryos. Our results indicate that Dnmt1 is involved in the repression of retroelements through DNA methylation in early mouse development.

Chromatin regulators: weaving epigenetic nets

2010 ◽  
Vol 1 (3-4) ◽  
pp. 225-238 ◽  
Author(s):  
Inmaculada Hernández-Muñoz
Keyword(s):  
Nucleosome Position ◽  
Histone Variants ◽  
Cellular Memory ◽  
Intrinsic Signals ◽  
Differentiated Cells ◽  
Chromatin Regulators ◽  
Genome Wide ◽  
Chromatin Regulator ◽  
A Genome ◽  
Multicellular Organisms

AbstractIn multicellular organisms differentiated cells must maintain their cellular memory, which will be faithfully inherited and maintained by their progeny. In addition, these specialized cells are exposed to specific environmental and cell-intrinsic signals and will have to appropriately respond to them. Some of these stimuli lead to changes in a subset of genes or to a genome-wide reprogramming of the cells that will remain after stimuli removal and, in some instances, will be inherited by the daughter cells. The molecular substrate that integrates cellular memory and plasticity is the chromatin, a complex of DNA and histones unique to eukaryotes. The nucleosome is the fundamental unit of the chromatin and nucleosomal organization defines different chromatin conformations. Chromatin regulators affect chromatin conformation and accessibility by covalently modifying the DNA or the histones, substituting histone variants, remodeling the nucleosome position or modulating chromatin looping and folding. These regulators frequently act in multiprotein complexes and highly specific interplays among chromatin marks and different chromatin regulators allow a remarkable array of possibilities. Therefore, chromatin regulator nets act to propagate the conformation of different chromatin regions through DNA replication and mitosis, and to remodel the chromatin fiber to regulate the accessibility of the DNA to transcription factors and to the transcription and repair machineries. Here, the state-of-the-art of the best-known chromatin regulators is reviewed.

scholarly journals Dppa2/4 Counteract De Novo Methylation to Establish a Permissive Epigenome for Development

2020 ◽  
Author(s):  
Kristjan H. Gretarsson ◽  
Jamie A. Hackett
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Developmental Competence ◽  
Epigenetic Memory ◽  
Mammalian Development ◽  
Dna Hypomethylation ◽  
Lineage Specification ◽  
Regulatory Pathways ◽  
Genome Wide ◽  
Early Mammalian Development

ABSTRACTEarly mammalian development entails genome-wide epigenome remodeling, including DNA methylation erasure and reacquisition, which facilitates developmental competence. To uncover the mechanisms that orchestrate DNA methylation (DNAme) dynamics, we coupled a single-cell ratiometric DNAme reporter with unbiased CRISPR screening in ESC. We identify key genes and regulatory pathways that drive global DNA hypomethylation, and characterise roles for Cop1 and Dusp6. We also identify Dppa2 and Dppa4 as essential safeguards of focal epigenetic states. In their absence, developmental genes and evolutionary-young LINE1 elements, which DPPA2 specifically binds, lose H3K4me3 and gain ectopic de novo DNA methylation in pluripotent cells. Consequently, lineage-associated genes (and LINE1) acquire a repressive epigenetic memory, which renders them incompetent for activation during future lineage-specification. Dppa2/4 thereby sculpt the pluripotent epigenome by facilitating H3K4me3 and bivalency to counteract de novo methylation; a function co-opted by evolutionary young LINE1 to evade epigenetic decommissioning.

Cell surface antigens in early mammalian development

1983 ◽  
Vol 41 ◽  
pp. 584-587
Author(s):  
Lincoln V. Johnson ◽  
Patricia G. Calarco ◽  
Syivia Ploack-Charcon
Keyword(s):  
Cell Surface ◽  
Specific Cell ◽  
Cell Surface Molecules ◽  
Embryonic Cells ◽  
Mammalian Development ◽  
Mouse Development ◽  
Cell Surface Antigens ◽  
Surface Molecules ◽  
Preimplantation Mouse ◽  
Or Organization

Cell surface molecules are known to be functionally important In a number of developmental systems. Molecular components of the cell surface may participate in Intercellular adhesion, recognition and communication. Reactions occur r Ing at the cell surface may also influence developmental events by Induci ng i ntracelIular changes In cellular metabolism and gene expression which may, In turn, alter the composition and/or organization of surface components. Sequences of reactions mediated by cell surface molecules are probably Important In directing undifferentiated embryonic cells along specific dlfferentlatlve pathways.In the early development of the mammal Ian embryo, important events occurring during the preimplantation period are likely to require the participation of specific cell surface molecules. For example, these are likely to Include sperm-egg attachment and fusion, Interbl astomere adhesion, blastulatlon, and attachment of the blastocyst to the uterine epithelium. During preimplantation mouse development, specific stage-relaged changes in the qual itatlve and quantitative nature of the proteins synthesized and those expressed on the cell surface have been documented.

QSER1 protects DNA methylation valleys from de novo methylation

Science ◽  
2021 ◽  
Vol 372 (6538) ◽  
pp. eabd0875 ◽  
Author(s):  
Gary Dixon ◽  
Heng Pan ◽  
Dapeng Yang ◽  
Bess P. Rosen ◽  
Therande Jashari ◽  
...  
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Embryonic Stem ◽  
Central Question ◽  
Mammalian Development ◽  
Uncharacterized Gene ◽  
Pathological Conditions ◽  
Genome Wide ◽  
A Genome ◽  
De Novo Methylation

DNA methylation is essential to mammalian development, and dysregulation can cause serious pathological conditions. Key enzymes responsible for deposition and removal of DNA methylation are known, but how they cooperate to regulate the methylation landscape remains a central question. Using a knockin DNA methylation reporter, we performed a genome-wide CRISPR-Cas9 screen in human embryonic stem cells to discover DNA methylation regulators. The top screen hit was an uncharacterized gene, QSER1, which proved to be a key guardian of bivalent promoters and poised enhancers of developmental genes, especially those residing in DNA methylation valleys (or canyons). We further demonstrate genetic and biochemical interactions of QSER1 and TET1, supporting their cooperation to safeguard transcriptional and developmental programs from DNMT3-mediated de novo methylation.

scholarly journals A framework for TRIM21-mediated protein depletion in early mouse embryos: recapitulation of Tead4 null phenotype over three days

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Steffen Israel ◽  
Ellen Casser ◽  
Hannes C.A. Drexler ◽  
Georg Fuellen ◽  
Michele Boiani
Keyword(s):  
Effective Means ◽  
Absolute Quantification ◽  
Mammalian Development ◽  
Mouse Development ◽  
Cell Stage ◽  
Knock Out ◽  
Protein Depletion ◽  
Dna And Rna ◽  
Gene And Protein Expression ◽  
Early Mouse

Abstract Background While DNA and RNA methods are routine to disrupt the expression of specific genes, complete understanding of developmental processes requires also protein methods, because: oocytes and early embryos accumulate proteins and these are not directly affected by DNA and RNA methods. When proteins in the oocyte encounter a specific antibody and the TRIpartite Motiv-containing 21 (TRIM21) ubiquitin-protein ligase, they can be committed to degradation in the proteasome, producing a transient functional knock-out that reveals the role of the protein. However, there are doubts about whether this targeted proteolysis could be successfully used to study mammalian development, because duration of the transient effect is unknown, and also because amounts of reagents delivered must be adequate in relation to the amount of target protein, which is unknown, too. Results We show that the mouse egg contains up to 1E-02 picomoles/protein, as estimated by mass spectrometry using the intensity-based absolute quantification (iBAQ) algorithm. However, the egg can only accommodate ≈1E-04 picomoles of antibody or TRIM21 without incurring toxic effects. Within this framework, we demonstrate that TRIM21-mediated protein depletion efficiently disrupts the embryonic process of trophectoderm formation, which critically depends on the TEA domain family member 4 (Tead4) gene. TEAD4 depletion starting at the 1-cell stage lasts for 3 days prior to a return of gene and protein expression to baseline. This time period is long enough to result in a phenotype entirely consistent with that of the published null mutation and RNA interference studies: significant underexpression of trophectodermal genes Cdx2 and Gata3 and strongly impaired ability of embryos to cavitate and implant in the uterus. Omics data are available via ProteomeXchange (PXD012613) and GEO (GSE124844). Conclusions TRIM21-mediated protein depletion can be an effective means to disrupt gene function in mouse development, provided the target gene is chosen carefully and the method is tuned accurately. The knowledge gathered in this study provides the basic know-how (prerequisites, requirements, limitations) to expedite the protein depletion of other genes besides Tead4.

Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development

Development ◽  
2000 ◽  
Vol 127 (8) ◽  
pp. 1737-1749 ◽  
Author(s):  
M.S. Ko ◽  
J.R. Kitchen ◽  
X. Wang ◽  
T.A. Threat ◽  
X. Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Disorders ◽  
Large Scale ◽  
Expression Patterns ◽  
Mammalian Development ◽  
Mouse Development ◽  
New Genes ◽  
Entry Points ◽  
Preimplantation Mouse ◽  
Mammalian Genes

Little is known about gene action in the preimplantation events that initiate mammalian development. Based on cDNA collections made from each stage from egg to blastocyst, 25438 3′-ESTs were derived, and represent 9718 genes, half of them novel. Thus, a considerable fraction of mammalian genes is dedicated to embryonic expression. This study reveals profound changes in gene expression that include the transient induction of transcripts at each stage. These results raise the possibility that development is driven by the action of a series of stage-specific expressed genes. The new genes, 798 of them placed on the mouse genetic map, provide entry points for analyses of human and mouse developmental disorders.

scholarly journals Transitions in cell potency during early mouse development are driven by Notch

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Sergio Menchero ◽  
Isabel Rollan ◽  
Antonio Lopez-Izquierdo ◽  
Maria Jose Andreu ◽  
Julio Sainz de Aja ◽  
...  
Keyword(s):  
Cell Fate ◽  
Cell Types ◽  
Mammalian Development ◽  
Mouse Development ◽  
Cell Stage ◽  
Notch Signalling Pathway ◽  
Gradual Loss ◽  
Early Mouse

The Notch signalling pathway plays fundamental roles in diverse developmental processes in metazoans, where it is important in driving cell fate and directing differentiation of various cell types. However, we still have limited knowledge about the role of Notch in early preimplantation stages of mammalian development, or how it interacts with other signalling pathways active at these stages such as Hippo. By using genetic and pharmacological tools in vivo, together with image analysis of single embryos and pluripotent cell culture, we have found that Notch is active from the 4-cell stage. Transcriptomic analysis in single morula identified novel Notch targets, such as early naïve pluripotency markers or transcriptional repressors such as TLE4. Our results reveal a previously undescribed role for Notch in driving transitions during the gradual loss of potency that takes place in the early mouse embryo prior to the first lineage decisions.

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