scholarly journals The Dynamic 3D Genome in Gametogenesis and Early Embryonic Development

Cells ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 788 ◽  
Author(s):  
Li ◽  
An ◽  
Zhang
Keyword(s):  
Developmental Biology ◽  
Embryonic Development ◽  
Research Methods ◽  
Chromatin Structure ◽  
Model Systems ◽  
Early Embryonic Development ◽  
3D Genome ◽  
Input Material ◽  
3D Chromatin Structure ◽  
And Function

During gametogenesis and early embryonic development, the chromatin architecture changes dramatically, and both the transcriptomic and epigenomic landscape are comprehensively reprogrammed. Understanding these processes is the holy grail in developmental biology and a key step towards evolution. The 3D conformation of chromatin plays a central role in the organization and function of nuclei. Recently, the dynamics of chromatin structures have been profiled in many model and non-model systems, from insects to mammals, resulting in an interesting comparison. In this review, we first introduce the research methods of 3D chromatin structure with low-input material suitable for embryonic study. Then, the dynamics of 3D chromatin architectures during gametogenesis and early embryonic development is summarized and compared between species. Finally, we discuss the possible mechanisms for triggering the formation of genome 3D conformation in early development.

scholarly journals Impact of DNA methylation on 3D genome structure

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Diana Buitrago ◽  
Mireia Labrador ◽  
Juan Pablo Arcon ◽  
Rafael Lema ◽  
Oscar Flores ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Chromatin Structure ◽  
Chromatin Condensation ◽  
Genome Structure ◽  
Dna Methyltransferases ◽  
Model System ◽  
Structure And Function ◽  
3D Genome ◽  
Cellular Machinery ◽  
And Function

AbstractDetermining the effect of DNA methylation on chromatin structure and function in higher organisms is challenging due to the extreme complexity of epigenetic regulation. We studied a simpler model system, budding yeast, that lacks DNA methylation machinery making it a perfect model system to study the intrinsic role of DNA methylation in chromatin structure and function. We expressed the murine DNA methyltransferases in Saccharomyces cerevisiae and analyzed the correlation between DNA methylation, nucleosome positioning, gene expression and 3D genome organization. Despite lacking the machinery for positioning and reading methylation marks, induced DNA methylation follows a conserved pattern with low methylation levels at the 5’ end of the gene increasing gradually toward the 3’ end, with concentration of methylated DNA in linkers and nucleosome free regions, and with actively expressed genes showing low and high levels of methylation at transcription start and terminating sites respectively, mimicking the patterns seen in mammals. We also see that DNA methylation increases chromatin condensation in peri-centromeric regions, decreases overall DNA flexibility, and favors the heterochromatin state. Taken together, these results demonstrate that methylation intrinsically modulates chromatin structure and function even in the absence of cellular machinery evolved to recognize and process the methylation signal.

scholarly journals The Birth of the 3D Genome during Early Embryonic Development

2018 ◽  
Vol 34 (12) ◽  
pp. 903-914 ◽  
Author(s):  
Clemens B. Hug ◽  
Juan M. Vaquerizas
Keyword(s):  
Embryonic Development ◽  
Early Embryonic Development ◽  
3D Genome

Analysis of hpf1 expression and function in early embryonic development of zebrafish

2018 ◽  
Vol 228 (2) ◽  
pp. 141-147 ◽  
Author(s):  
Zhen Zhang ◽  
Hongwei Sun ◽  
Yu Chen ◽  
Tianqi Cao ◽  
Zhou Songyang ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Early Embryonic Development ◽  
And Function

scholarly journals DEAD-Box Protein-103 (DP103, Ddx20) Is Essential for Early Embryonic Development and Modulates Ovarian Morphology and Function

Endocrinology ◽  
2008 ◽  
Vol 149 (5) ◽  
pp. 2168-2175 ◽  
Author(s):  
Jean-François Mouillet ◽  
Xiaomei Yan ◽  
Qinglin Ou ◽  
Lingling Jin ◽  
Louis J. Muglia ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Micro Rna ◽  
Early Embryonic Development ◽  
Cell Stage ◽  
Steroidogenic Factor 1 ◽  
Multifunctional Protein ◽  
Barr Virus ◽  
Dead Box ◽  
Epstein Barr ◽  
And Function

The DEAD-box helicase DP103 (Ddx20, Gemin3) is a multifunctional protein that interacts with Epstein-Barr virus nuclear proteins (EBNA2/EBNA3) and is a part of the spliceosomal small nuclear ribonucleoproteins complex. DP103 also aggregates with the micro-RNA machinery complex. We have previously shown that DP103 interacts with the nuclear receptor steroidogenic factor-1 (SF-1, NR5A1), a key regulator of reproductive development, and represses its transcriptional activity. To further explore the physiological function of DP103, we disrupted the corresponding gene in mice. Homozygous Dp103-null mice die early in embryonic development before a four-cell stage. Although heterozygous mice are healthy and fertile, analysis of steroidogenic tissues revealed minor abnormalities in mutant females, including larger ovaries, altered estrous cycle, and reduced basal secretion of ACTH. Our data point to diverse functions of murine DP103, with an obligatory role during early embryonic development and also in modulation of steroidogenesis.

Dynamic reprogramming and function of RNA N6-methyladenosine modification during porcine early embryonic development

Zygote ◽  
2021 ◽  
pp. 1-10
Author(s):  
Tong Yu ◽  
Xin Qi ◽  
Ling Zhang ◽  
Wei Ning ◽  
Di Gao ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Pluripotent Stem Cells ◽  
Somatic Cell Nuclear Transfer ◽  
Nuclear Transfer ◽  
Early Embryonic Development ◽  
Parthenogenetic Activation ◽  
Methylation Inhibitor ◽  
Induced Pluripotent ◽  
And Function

Summary N6-Methyladenosine (m6A) regulates oocyte-to-embryo transition and the reprogramming of somatic cells into induced pluripotent stem cells. However, the role of m6A methylation in porcine early embryonic development and its reprogramming characteristics in somatic cell nuclear transfer (SCNT) embryos are yet to be known. Here, we showed that m6A methylation was essential for normal early embryonic development and its aberrant reprogramming in SCNT embryos. We identified a persistent occurrence of m6A methylation in embryos between 1-cell to blastocyst stages and m6A levels abruptly increased during the morula-to-blastocyst transition. Cycloleucine (methylation inhibitor, 20 mM) treatment efficiently reduced m6A levels, significantly decreased the rates of 4-cell embryos and blastocysts, and disrupted normal lineage allocation. Moreover, cycloleucine treatment also led to higher levels in both apoptosis and autophagy in blastocysts. Furthermore, m6A levels in SCNT embryos at the 4-cell and 8-cell stages were significantly lower than that in parthenogenetic activation (PA) embryos, suggesting an abnormal reprogramming of m6A methylation in SCNT embryos. Correspondingly, expression levels of m6A writers (METTL3 and METTL14) and eraser (FTO) were apparently higher in SCNT 8-cell embryos compared with their PA counterparts. Taken together, these results indicated that aberrant nuclear transfer-mediated reprogramming of m6A methylation was involved in regulating porcine early embryonic development.

scholarly journals Actomyosin controls planarity and folding of epithelia in response to compression

2018 ◽  
Author(s):  
Tom P. J. Wyatt ◽  
Jonathan Fouchard ◽  
Ana Lisica ◽  
Nargess Khalilgharibi ◽  
Buzz Baum ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Embryonic Development ◽  
Adult Life ◽  
Model Systems ◽  
Profound Impact ◽  
Automatic Adaptation ◽  
External Forces ◽  
And Function ◽  
Actomyosin Cytoskeleton ◽  
Cell Extrusion

ABSTRACTThroughout embryonic development and adult life, epithelia are subjected to external forces. The resulting deformations can have a profound impact on tissue development and function. These include compressive deformations which, although hard to study in model systems due to the confounding effects of the substrate, are thought to play an important role in tissue morphogenesis by inducing tissue folding and by triggering mechanosensitive responses including cell extrusion and cell differentiation. Here, using suspended epithelia, we are able to uncover the immediate response of epithelial tissues to the application of large (5-80%) in-plane compressive strains. We show that fast compression induces tissue buckling followed by active tissue flattening which erases the buckle within tens of seconds. Strikingly, there is a well-defined limit to this second response, so that stable folds form in the tissue for compressive strains larger than ∼35%. Finally, a combination of experiment and modelling shows that the response to compression is orchestrated by the automatic adaptation of the actomyosin cytoskeleton as it re-establishes tension in compressed tissues. Thus, tissue pre-tension allows epithelia to both buffer against fast compression and regulate folding.

scholarly journals Establishment of 3D chromatin structure after fertilization and the metabolic switch at the morula-to-blastocyst transition require CTCF

2021 ◽  
Author(s):  
Maria Jose Andreu ◽  
Alba Alvarez-Franco ◽  
Marta Portela ◽  
Daniel Gimenez-Llorente ◽  
Ana Cuadrado ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Zinc Finger Protein ◽  
De Novo ◽  
Genome Structure ◽  
Blastocyst Stage ◽  
Mammalian Development ◽  
Metabolic Switch ◽  
3D Genome ◽  
3D Chromatin Structure ◽  
The Impact

The eukaryotic genome is tightly packed inside the nucleus, where it is organized in 3D at different scales. This structure is driven and maintained by different chromatin states and by architectural factors that bind DNA, such as the multi-zinc finger protein CTCF. Zygotic genome structure is established de novo after fertilization, but the impact of such structure on genome function during the first stages of mammalian development is still unclear. Here, we show that deletion of the Ctcf gene in mouse embryos impairs the correct establishment of chromatin structure, but initial lineage decisions take place and embryos are viable until the late blastocyst stage. Furthermore, we observe that maternal CTCF is not necessary for development. Transcriptomic analyses of mutant embryos show that the changes in metabolic and protein homeostasis programs that occur during the progression from the morula to the blastocyst depend on CTCF. Yet, these changes in gene expression do not correlate with disruption of chromatin structure, but mainly with proximal binding of CTCF to the promoter region of genes downregulated in mutants. Our results show that CTCF regulates both 3D genome organization and transcription during mouse preimplantation development, but mostly as independent processes.

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