scholarly journals Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis

PLoS ONE ◽  
2015 ◽  
Vol 10 (9) ◽  
pp. e0137526 ◽  
Author(s):  
Nicolas Buisine ◽  
Xiaoan Ruan ◽  
Patrice Bilesimo ◽  
Alexis Grimaldi ◽  
Gladys Alfama ◽  
...  
Keyword(s):  
Xenopus Tropicalis ◽  
Tropicalis Genome

scholarly journals Identification of REST targets in the Xenopus tropicalis genome

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Banu Saritas-Yildirim ◽  
Christopher P Childers ◽  
Christine G Elsik ◽  
Elena M Silva
Keyword(s):  
Xenopus Tropicalis ◽  
Tropicalis Genome

The Xenopus Tropicalis Genome Project

2003 ◽  
Vol 4 (8) ◽  
pp. 645-652 ◽  
Author(s):  
Paul Richardson ◽  
Jarrod Chapman
Keyword(s):  
Genome Project ◽  
Xenopus Tropicalis ◽  
Tropicalis Genome

scholarly journals Three-dimensional folding dynamics of the Xenopus tropicalis genome

2021 ◽  
Author(s):  
Longjian Niu ◽  
Wei Shen ◽  
Zhaoying Shi ◽  
Yongjun Tan ◽  
Na He ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Transcriptional Activation ◽  
De Novo ◽  
Three Dimensional ◽  
Xenopus Tropicalis ◽  
Chromosome Conformation ◽  
Chromosome Architecture ◽  
Tropicalis Genome ◽  
Architectural Proteins ◽  
Folding Dynamics

AbstractAnimal interphase chromosomes are organized into topologically associating domains (TADs). How TADs are formed is not fully understood. Here, we combined high-throughput chromosome conformation capture and gene silencing to obtain insights into TAD dynamics in Xenopus tropicalis embryos. First, TAD establishment in X. tropicalis is similar to that in mice and flies and does not depend on zygotic genome transcriptional activation. This process is followed by further refinements in active and repressive chromatin compartments and the appearance of loops and stripes. Second, within TADs, higher self-interaction frequencies at one end of the boundary are associated with higher DNA occupancy of the architectural proteins CTCF and Rad21. Third, the chromatin remodeling factor ISWI is required for de novo TAD formation. Finally, TAD structures are variable in different tissues. Our work shows that X. tropicalis is a powerful model for chromosome architecture analysis and suggests that chromatin remodeling plays an essential role in de novo TAD establishment.

scholarly journals Epithelial-Mesenchymal Transition Promotes the Differentiation Potential of Xenopus tropicalis Immature Sertoli Cells

2019 ◽  
Vol 2019 ◽  
pp. 1-16 ◽  
Author(s):  
Thi Minh Xuan Nguyen ◽  
Marketa Vegrichtova ◽  
Tereza Tlapakova ◽  
Magdalena Krulova ◽  
Vladimir Krylov
Keyword(s):  
Sertoli Cells ◽  
Epithelial Mesenchymal Transition ◽  
Day Treatment ◽  
Xenopus Tropicalis ◽  
Differentiation Potential ◽  
Mesenchymal Transition ◽  
Fundamental Process

Epithelial-mesenchymal transition (EMT) is a fundamental process in embryonic development by which sessile epithelial cells are converted into migratory mesenchymal cells. Our laboratory has been successful in the establishment of Xenopus tropicalis immature Sertoli cells (XtiSCs) with the restricted differentiation potential. The aim of this study is the determination of factors responsible for EMT activation in XtiSCs and stemness window acquisition where cells possess the broadest differentiation potential. For this purpose, we tested three potent EMT inducers—GSK-3 inhibitor (CHIR99021), FGF2, and/or TGF-β1 ligand. XtiSCs underwent full EMT after 3-day treatment with CHIR99021 and partial EMT with FGF2 but not with TGF-β1. The morphological change of CHIR-treated XtiSCs to the typical spindle-like cell shape was associated with the upregulation of mesenchymal markers and the downregulation of epithelial markers. Moreover, only CHIR-treated XtiSCs were able to differentiate into chondrocytes in vitro and cardiomyocytes in vivo. Interestingly, EMT-shifted cells could migrate towards cancer cells (HeLa) in vitro and to the injury site in vivo. The results provide a better understanding of signaling pathways underlying the generation of testis-derived stem cells.

scholarly journals Developmental Regulation and Function of Thyroid Hormone Receptors and 9-cis Retinoic Acid Receptors during Xenopus tropicalis Metamorphosis

Endocrinology ◽  
2008 ◽  
Vol 149 (11) ◽  
pp. 5610-5618 ◽  
Author(s):  
Xuedong Wang ◽  
Hiroki Matsuda ◽  
Yun-Bo Shi
Keyword(s):  
Retinoic Acid ◽  
Genomic Sequence ◽  
Expression Profiles ◽  
Postembryonic Development ◽  
Xenopus Tropicalis ◽  
Retinoic Acid Receptors ◽  
Developmental Cycle ◽  
Sequence Information ◽  
And Function

Amphibian metamorphosis serves as an excellent model to study T3 function during postembryonic development in vertebrate due to its total dependence on T3. Earlier molecular studies in the model species Xenopus laevis have led to a number of important in vivo findings on the function and mechanisms of T3 receptor (TR) action during vertebrate development. However, the lack of genomic sequence information, its tetraploid genome, and lengthy developmental cycle hinder further analyses on TR functions. In this regard, the highly related species, Xenopus tropicalis, is much more advantageous. Toward developing X. tropicalis for genome-wide and genetic studies of TR function, we analyzed the expression profiles of TRs and their heterodimerization partners, retinoid X receptors (RXRs) or 9-cis retinoic acid receptors. We show that their expression correlates with transformations in different organs and that TR/RXR heterodimers are capable of repressing and activating gene expression in vivo in the absence and presence of T3, respectively. We further demonstrate that TRs are bound to endogenous target genes in X. tropicalis tadpoles. Our results thus support a role of TRs in mediating the metamorphic effects of T3 in X. tropicalis. More importantly, the similarities in the expression and function between X. tropicalis and X. laevis TRs and RXRs as demonstrated by our study also pave the way to take advantages of existing morphological, molecular, and cellular knowledge of X. laevis development and the genetic and sequence superiority of X. tropicalis to dissect the molecular pathways governing tissue/organ-specific transformations during vertebrate postembryonic development.

scholarly journals The development of Xenopus tropicalis transgenic lines and their use in studying lens developmental timing in living embryos

Development ◽  
2000 ◽  
Vol 127 (9) ◽  
pp. 1789-1797 ◽  
Author(s):  
M.F. Offield ◽  
N. Hirsch ◽  
R.M. Grainger
Keyword(s):  
Transgenic Animals ◽  
Xenopus Tropicalis ◽  
Close Relative ◽  
Gfp Reporter ◽  
Tissue Manipulation ◽  
External Cues ◽  
New Strategy ◽  
Transgenic Lines ◽  
In Vivo Analysis

The generation of reporter lines for observing lens differentiation in vivo demonstrates a new strategy for embryological manipulation and allows us to address a long-standing question concerning the timing of the onset of differentiation. Xenopus tropicalis was used to make GFP reporter lines with (gamma)1-crystallin promoter elements directing GFP expression within the early lens. X. tropicalis is a close relative of X. laevis that shares the same ease of tissue manipulation with the added benefits of a diploid genome and faster life cycle. The efficiency of the Xenopus transgenic technique was improved in order to generate greater numbers of normal, adult transgenic animals and to facilitate in vivo analysis of the crystallin promoter. This transgene is transmitted through the germline, providing an accurate and consistent way to monitor lens differentiation. This line permitted us to distinguish models for how the onset of differentiation is controlled: by a process intrinsic to differentiating tissue or one dependent on external cues. This experiment would not have been feasible without the sensitivity and accuracy provided by the in vivo reporter. We find that, in specified lens ectoderm transplanted from neural tube stage donors to younger neural-plate-stage hosts, the onset of differentiation, as measured by expression of the crystallin/GFP transgene, is delayed by an average of 4.4 hours. When specified lens ectoderm is explanted into culture, the delay was an average of 16.3 hours relative to control embryos. These data suggest that the onset of differentiation in specified ectoderm can be altered by the environment and imply that this onset is normally controlled by external cues rather than by an intrinsic mechanism.

In-vivo regulation of Krüppel-like factor 9 by corticosteroids and their receptors across tissues in tadpoles of Xenopus tropicalis

2017 ◽  
Vol 248 ◽  
pp. 79-86 ◽  
Author(s):  
Leena H. Shewade ◽  
Katelin A. Schneider ◽  
Audrey C. Brown ◽  
Daniel R. Buchholz
Keyword(s):  
Xenopus Tropicalis

Fine Structural Changes in the Microvasculature of the Mouse Pinna: Aging and Radiation Injury

1974 ◽  
Vol 32 ◽  
pp. 54-55
Author(s):  
S. Phyllis Steamer ◽  
Rosemarie L. Devine
Keyword(s):  
Structural Changes ◽  
Radiation Treatment ◽  
Arterial Stenosis ◽  
Ultrastructural Changes ◽  
Vascular Effects ◽  
Microvascular Changes ◽  
Surrounding Connective Tissue ◽  
Fission Neutrons ◽  
Total Body

The importance of radiation damage to the skin and its vasculature was recognized by the early radiologists. In more recent studies, vascular effects were shown to involve the endothelium as well as the surrounding connective tissue. Microvascular changes in the mouse pinna were studied in vivo and recorded photographically over a period of 12-18 months. Radiation treatment at 110 days of age was total body exposure to either 240 rad fission neutrons or 855 rad 60Co gamma rays. After in vivo observations in control and irradiated mice, animals were sacrificed for examination of changes in vascular fine structure. Vessels were selected from regions of specific interest that had been identified on photomicrographs. Prominent ultrastructural changes can be attributed to aging as well as to radiation treatment. Of principal concern were determinations of ultrastructural changes associated with venous dilatations, segmental arterial stenosis and tortuosities of both veins and arteries, effects that had been identified on the basis of light microscopic observations. Tortuosities and irregularly dilated vein segments were related to both aging and radiation changes but arterial stenosis was observed only in irradiated animals.

Induction and Differentiation of Dental Epithelium in Vivo and in Vitro

1982 ◽  
Vol 40 ◽  
pp. 142-145
Author(s):  
E. J. Kollar
Keyword(s):  
Connective Tissue ◽  
Oral Mucosa ◽  
Basal Lamina ◽  
Functional Derivatives ◽  
Specific Source ◽  
Dental Epithelium ◽  
Connective Tissue Stroma

The differentiation and maintenance of many specialized epithelial structures are dependent on the underlying connective tissue stroma and on an intact basal lamina. These requirements are especially stringent in the development and maintenance of the skin and oral mucosa. The keratinization patterns of thin or thick cornified layers as well as the appearance of specialized functional derivatives such as hair and teeth can be correlated with the specific source of stroma which supports these differentiated expressions.

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