scholarly journals Spemann organizer transcriptome induction by early beta-catenin, Wnt, Nodal, and Siamois signals in Xenopus laevis

2017 ◽  
Vol 114 (15) ◽  
pp. E3081-E3090 ◽  
Author(s):  
Yi Ding ◽  
Diego Ploper ◽  
Eric A. Sosa ◽  
Gabriele Colozza ◽  
Yuki Moriyama ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Gene Signature ◽  
Dorsal Side ◽  
Beta Catenin ◽  
Loss Of Function ◽  
Spemann Organizer ◽  
Signature Genes ◽  
A Genome ◽  
Vertebrate Model ◽  
Chloride Treatment

The earliest event in Xenopus development is the dorsal accumulation of nuclear β-catenin under the influence of cytoplasmic determinants displaced by fertilization. In this study, a genome-wide approach was used to examine transcription of the 43,673 genes annotated in the Xenopus laevis genome under a variety of conditions that inhibit or promote formation of the Spemann organizer signaling center. Loss of function of β-catenin with antisense morpholinos reproducibly reduced the expression of 247 mRNAs at gastrula stage. Interestingly, only 123 β-catenin targets were enriched on the dorsal side and defined an early dorsal β-catenin gene signature. These genes included several previously unrecognized Spemann organizer components. Surprisingly, only 3 of these 123 genes overlapped with the late Wnt signature recently defined by two other groups using inhibition by Dkk1 mRNA or Wnt8 morpholinos, which indicates that the effects of β-catenin/Wnt signaling in early development are exquisitely regulated by stage-dependent mechanisms. We analyzed transcriptome responses to a number of treatments in a total of 46 RNA-seq libraries. These treatments included, in addition to β-catenin depletion, regenerating dorsal and ventral half-embryos, lithium chloride treatment, and the overexpression of Wnt8, Siamois, and Cerberus mRNAs. Only some of the early dorsal β-catenin signature genes were activated at blastula whereas others required the induction of endomesoderm, as indicated by their inhibition by Cerberus overexpression. These comprehensive data provide a rich resource for analyzing how the dorsal and ventral regions of the embryo communicate with each other in a self-organizing vertebrate model embryo.

scholarly journals SP8 Promotes an Aggressive Phenotype in Hepatoblastoma via FGF8 Activation

Cancers ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 2294
Author(s):  
Alexandra Elisabeth Wagner ◽  
Thomas Schwarzmayr ◽  
Beate Häberle ◽  
Christian Vokuhl ◽  
Irene Schmid ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Epithelial Mesenchymal Transition ◽  
Gene Signature ◽  
Good Prognosis ◽  
Significant Inhibition ◽  
Loss Of Function ◽  
Promoter Regions ◽  
Malignant Liver Tumor ◽  
Mesenchymal Transition ◽  
A Genome

Hepatoblastoma (HB) is the most common malignant liver tumor in childhood and it generally has a good prognosis. However, if associated with aggressive metastatic disease, outcome is still poor. The molecular mechanisms leading to metastatic spread in HB patients are still unknown. By combining RNA-sequencing and a genome-wide methylome analysis, we identified the transcription factor SP8 and the growth factor FGF8 among the most strongly upregulated genes in metastatic HB cases, with a concomitant robust demethylation of the respective promoter regions. Of note, high expression of both candidates was associated with the aggressive C2 subtype of the 16-gene signature and poor survival. Chromatin immunoprecipitation revealed a direct transcriptional regulation of FGF8 through binding of SP8 to the FGF8 promoter. Gain- and loss-of-function experiments proved promoting effects of SP8 on motility, self-renewal, migration, and the invasive potential of HB cells. Moreover, stable overexpression of SP8 in Hep3B cells resulted in the acquisition of a mesenchymal phenotype and a strong upregulation of epithelial-mesenchymal transition-associated genes. Using KRAB-mediated CRISPR-dCas9 interference directed against FGF8, we could show that FGF8 is essential for the SP8-mediated aggressive tumor behavior. Treatment of HB cell lines with the pan SP family inhibitor mithramycin A resulted in a significant inhibition of their clonogenic growth. In summary, we identified SP8 and FGF8 as key players in aggressive traits of HB and propose SP8 inhibiting drugs as a new effective treatment strategy especially for metastatic tumors.

scholarly journals A Nonsense Variant in Hephaestin Like 1 (HEPHL1) Is Responsible for Congenital Hypotrichosis in Belted Galloway Cattle

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 643
Author(s):  
Thibaud Kuca ◽  
Brandy M. Marron ◽  
Joana G. P. Jacinto ◽  
Julia M. Paris ◽  
Christian Gerspach ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Homozygosity Mapping ◽  
Mendelian Inheritance ◽  
Large Animal Model ◽  
Large Animal ◽  
Loss Of Function ◽  
Protein Coding ◽  
Positional Candidate ◽  
Genome Wide ◽  
A Genome

Genodermatosis such as hair disorders mostly follow a monogenic mode of inheritance. Congenital hypotrichosis (HY) belong to this group of disorders and is characterized by abnormally reduced hair since birth. The purpose of this study was to characterize the clinical phenotype of a breed-specific non-syndromic form of HY in Belted Galloway cattle and to identify the causative genetic variant for this recessive disorder. An affected calf born in Switzerland presented with multiple small to large areas of alopecia on the limbs and on the dorsal part of the head, neck, and back. A genome-wide association study using Swiss and US Belted Galloway cattle encompassing 12 cases and 61 controls revealed an association signal on chromosome 29. Homozygosity mapping in a subset of cases refined the HY locus to a 1.5 Mb critical interval and subsequent Sanger sequencing of protein-coding exons of positional candidate genes revealed a stop gain variant in the HEPHL1 gene that encodes a multi-copper ferroxidase protein so-called hephaestin like 1 (c.1684A>T; p.Lys562*). A perfect concordance between the homozygous presence of this most likely pathogenic loss-of-function variant and the HY phenotype was found. Genotyping of more than 700 purebred Swiss and US Belted Galloway cattle showed the global spread of the mutation. This study provides a molecular test that will permit the avoidance of risk matings by systematic genotyping of relevant breeding animals. This rare recessive HEPHL1-related form of hypotrichosis provides a novel large animal model for similar human conditions. The results have been incorporated in the Online Mendelian Inheritance in Animals (OMIA) database (OMIA 002230-9913).

Activation of dorsal development by contact between the cortical dorsal determinant and the equatorial core cytoplasm in eggs of Xenopus laevis

Development ◽  
1997 ◽  
Vol 124 (8) ◽  
pp. 1543-1551 ◽  
Author(s):  
H. Kageura
Keyword(s):  
Xenopus Laevis ◽  
Dorsal Side ◽  
Equatorial Region ◽  
Normal Embryo ◽  
Dorsal Region ◽  
The Core ◽  
Dorsal Axis ◽  
The Future ◽  
Vegetal Pole ◽  
Cell Embryo

In eggs of Xenopus laevis, dorsal development is activated on the future dorsal side by cortical rotation, after fertilization. The immediate effect of cortical rotation is probably the transport of a dorsal determinant from the vegetal pole to the equatorial region on the future dorsal side. However, the identity and action of the dorsal determinant remain problematic. In the present experiments, individual isolated cortices from various regions of the unfertilized eggs and embryos were implanted into one of several positions of a recipient 8-cell embryo. The incidence of secondary axes was used not only to locate the cortical dorsal determinant at different times but also to locate the region of the core competent to respond to the dorsal determinant. The dorsal axis-inducing activity of the cortex occurred around the vegetal pole of the unfertilized egg. During cortical rotation, it shifted from there to a wide dorsal region. This is apparently the first evidence for the presence of a dorsal determinant in the egg cortex. The competence of the core of the 8-cell embryo was distributed in the form of gradient with the highest responsiveness at the equator. These results suggest that, in the normal embryo, dorsal development is activated by contact between the cortical dorsal determinant and the equatorial core cytoplasm, brought together through cortical rotation.

scholarly journals 16p12.1 deletion orthologs are expressed in motile neural crest cells and are important for regulating craniofacial development in Xenopus laevis

2020 ◽  
Author(s):  
Micaela Lasser ◽  
Jessica Bolduc ◽  
Luke Murphy ◽  
Caroline O'Brien ◽  
Sangmook Lee ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Neural Crest ◽  
Expression Patterns ◽  
Copy Number Variants ◽  
Neural Crest Cell ◽  
Underlying Mechanism ◽  
Craniofacial Development ◽  
Pharyngeal Arches ◽  
Individual Gene ◽  
Vertebrate Model

Copy number variants (CNVs) associated with neurodevelopmental disorders are characterized by extensive phenotypic heterogeneity. In particular, one CNV was identified in a subset of children clinically diagnosed with intellectual disabilities (ID) that results in a hemizygous deletion of multiple genes at chromosome 16p12.1. In addition to ID, individuals with this deletion display a variety of symptoms including microcephaly, seizures, cardiac defects, and growth retardation. Moreover, patients also manifest severe craniofacial abnormalities, such as micrognathia, cartilage malformation of the ears and nose, and facial asymmetries; however, the function of the genes within the 16p12.1 region have not been studied in the context of vertebrate craniofacial development. The craniofacial tissues affected in patients with this deletion all derive from the same embryonic precursor, the cranial neural crest, leading to the hypothesis that one or more of the 16p12.1 genes may be involved in regulating neural crest cell (NCC)-related processes. To examine this, we characterized the developmental role of the 16p12.1-affected gene orthologs, polr3e, mosmo, uqcrc2, and cdr2, during craniofacial morphogenesis in the vertebrate model system, Xenopus laevis. While the currently-known cellular functions of these genes are diverse, we find that they share similar expression patterns along the neural tube, pharyngeal arches, and later craniofacial structures. As these genes show co-expression in the pharyngeal arches where NCCs reside, we sought to elucidate the effect of individual gene depletion on craniofacial development and NCC migration. We find that reduction of several 16p12.1 genes significantly disrupts craniofacial and cartilage formation, pharyngeal arch migration, as well as NCC specification and motility. Thus, we have determined that some of these genes play an essential role during vertebrate craniofacial patterning by regulating specific processes during NCC development, which may be an underlying mechanism contributing to the craniofacial defects associated with the 16p12.1 deletion.

scholarly journals Tumor-suppressor function of Beclin 1 in breast cancer cells requires E-cadherin

2021 ◽  
Vol 118 (5) ◽  
pp. e2020478118
Author(s):  
Tobias Wijshake ◽  
Zhongju Zou ◽  
Beibei Chen ◽  
Lin Zhong ◽  
Guanghua Xiao ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Tumor Suppressor ◽  
Cancer Cells ◽  
Breast Cancer Cells ◽  
Target Genes ◽  
Cellular Proliferation ◽  
Beclin 1 ◽  
Beta Catenin ◽  
A Genome ◽  
E Cadherin

Beclin 1, an autophagy and haploinsufficient tumor-suppressor protein, is frequently monoallelically deleted in breast and ovarian cancers. However, the precise mechanisms by which Beclin 1 inhibits tumor growth remain largely unknown. To address this question, we performed a genome-wide CRISPR/Cas9 screen in MCF7 breast cancer cells to identify genes whose loss of function reverse Beclin 1-dependent inhibition of cellular proliferation. Small guide RNAs targeting CDH1 and CTNNA1, tumor-suppressor genes that encode cadherin/catenin complex members E-cadherin and alpha-catenin, respectively, were highly enriched in the screen. CRISPR/Cas9-mediated knockout of CDH1 or CTNNA1 reversed Beclin 1-dependent suppression of breast cancer cell proliferation and anchorage-independent growth. Moreover, deletion of CDH1 or CTNNA1 inhibited the tumor-suppressor effects of Beclin 1 in breast cancer xenografts. Enforced Beclin 1 expression in MCF7 cells and tumor xenografts increased cell surface localization of E-cadherin and decreased expression of mesenchymal markers and beta-catenin/Wnt target genes. Furthermore, CRISPR/Cas9-mediated knockout of BECN1 and the autophagy class III phosphatidylinositol kinase complex 2 (PI3KC3-C2) gene, UVRAG, but not PI3KC3-C1–specific ATG14 or other autophagy genes ATG13, ATG5, or ATG7, resulted in decreased E-cadherin plasma membrane and increased cytoplasmic E-cadherin localization. Taken together, these data reveal previously unrecognized cooperation between Beclin 1 and E-cadherin–mediated tumor suppression in breast cancer cells.

scholarly journals A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Mark F Sabbagh ◽  
Jeremy Nathans
Keyword(s):  
Central Nervous System ◽  
Endothelial Cells ◽  
Nervous System ◽  
In Vitro Culture ◽  
Vascular Endothelial Cells ◽  
Beta Catenin ◽  
A Genome ◽  
Accessible Chromatin

Vascular endothelial cells (ECs) derived from the central nervous system (CNS) variably lose their unique barrier properties during in vitro culture, hindering the development of robust assays for blood-brain barrier (BBB) function, including drug permeability and extrusion assays. In previous work (Sabbagh et al., 2018) we characterized transcriptional and accessible chromatin landscapes of acutely isolated mouse CNS ECs. In this report, we compare transcriptional and accessible chromatin landscapes of acutely isolated mouse CNS ECs versus mouse CNS ECs in short-term in vitro culture. We observe that standard culture conditions are associated with a rapid and selective loss of BBB transcripts and chromatin features, as well as a greatly reduced level of beta-catenin signaling. Interestingly, forced expression of a stabilized derivative of beta-catenin, which in vivo leads to a partial conversion of non-BBB CNS ECs to a BBB-like state, has little or no effect on gene expression or chromatin accessibility in vitro.

A cytoplasmic determinant for dorsal axis formation in an early embryo of Xenopus laevis

Development ◽  
1990 ◽  
Vol 110 (4) ◽  
pp. 1051-1056 ◽  
Author(s):  
M. Yuge ◽  
Y. Kobayakawa ◽  
M. Fujisue ◽  
K. Yamana
Keyword(s):  
Xenopus Laevis ◽  
Direct Evidence ◽  
Early Embryo ◽  
Dorsal Side ◽  
Axis Formation ◽  
Secondary Axis ◽  
Dorsal Axis ◽  
Cell Embryo ◽  
Dorsal Cells ◽  
Cytoplasmic Determinant

In Xenopus laevis, dorsal cells that arise at the future dorsal side of an early cleaving embryo have already acquired the ability to cause axis formation. Since the distribution of cytoplasmic components is markedly heterogeneous in an egg and embryo, it has been supposed that the dorsal cells are endowed with the activity to form axial structures by inheriting a unique cytoplasmic component or components localized in the dorsal region of an egg or embryo. However, there has been no direct evidence for this. To examine the activity of the cytoplasm of dorsal cells, we injected cytoplasm (dorsal cytoplasm) from dorsal vegetal cells of a Xenopus 16-cell embryo into ventral vegetal cells of a simultaneous recipient. The cytoplasm caused secondary axis formation in 42% of recipients. Histological examination revealed that well-developed secondary axes included notochord, as well as a neural tube and somites. However, injection of cytoplasm of ventral vegetal cells never caused secondary axis and most recipients became normal tailbud embryos. Furthermore, about two-thirds of ventral isolated halves injected with dorsal cytoplasm formed axial structures. These results show that dorsal, but not ventral, cytoplasm contains the component or components responsible for axis formation. This can be the first step towards identifying the molecular basis of dorsal axis formation.

Identification and tissue expression profiling of candidate UDP-glycosyltransferase genes expressed in Holotrichia parallela motschulsky antennae

2018 ◽  
Vol 108 (6) ◽  
pp. 807-816 ◽  
Author(s):  
S. Wang ◽  
Y. Liu ◽  
J.-J. Zhou ◽  
J.-K. Yi ◽  
Y. Pan ◽  
...  
Keyword(s):  
Tissue Expression ◽  
Gene Signature ◽  
Structural Features ◽  
Water Soluble ◽  
Economic Losses ◽  
Uridine Diphosphate ◽  
Produce Water ◽  
Holotrichia Parallela ◽  
A Genome ◽  
Olfactory Tissue

AbstractIt is difficult to control Holotrichia parallela Motschulsky with chemical insecticides due to the larvae's soil-living habit, thus the pest has caused great economic losses in agriculture. In addition, uridine diphosphate-glycosyltransferases (UGTs) catalyze the glycosylation process of a variety of small lipophilic molecules with sugars to produce water-soluble glycosides, and play multiple roles in detoxification, endobiotic modulation, and sequestration in an insect. Some UGTs were found specifically expressed in antennae of Drosophila melanogaster and Spodoptera littoralis, and glucurono-conjugated odorants could not elicit any olfactory signals, suggesting that the UGTs may play roles in odorant inactivation by biotransformation. In the current study, we performed a genome-wide analysis of the candidate UGT family in the dark black chafer, H. parallela. Based on a UGT gene signature and the similarity of these genes to UGT homologs from other organisms, 20 putative H. parallela UGT genes were identified. Bioinformatics analysis was used to predict sequence and structural features of H. parallela UGT proteins, and revealed important domains and residues involved in sugar donor binding and catalysis by comparison with human UGT2B7. Phylogenetic analysis of these 20 UGT protein sequences revealed eight major groups, including both order-specific and conserved groups, which are common to more than one order. Of these 20 UGT genes, HparUGT1265-1, HparUGT3119, and HparUGT8312 were highly (>100-fold change) expressed in antennae, suggesting a possible role in olfactory tissue, and most likely in odorant inactivation and olfactory processing. The remaining UGT genes were expressed in all tissues (head, thorax, abdomen, leg, and wing), indicating that these UGTs likely have different biological functions. This study provides the fundamental basis for determining the function of UGTs in a highly specialized olfactory organ, the H. parallela antenna.

scholarly journals Generation and Transcriptome Profiling of Slr1-d7 and Slr1-d8 Mutant Lines with a New Semi-Dominant Dwarf Allele of SLR1 Using the CRISPR/Cas9 System in Rice

2020 ◽  
Vol 21 (15) ◽  
pp. 5492 ◽  
Author(s):  
Yu Jin Jung ◽  
Jong Hee Kim ◽  
Hyo Ju Lee ◽  
Dong Hyun Kim ◽  
Jihyeon Yu ◽  
...  
Keyword(s):  
Gene Expression Analysis ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Loss Of Function ◽  
Amino Acid Motif ◽  
Dwarf Phenotype ◽  
Genome Wide ◽  
A Genome ◽  
Mutant Lines ◽  
Genome Wide Gene Expression

The rice SLR1 gene encodes the DELLA protein (protein with DELLA amino acid motif), and a loss-of-function mutation is dwarfed by inhibiting plant growth. We generate slr1-d mutants with a semi-dominant dwarf phenotype to target mutations of the DELLA/TVHYNP domain using CRISPR/Cas9 genome editing in rice. Sixteen genetic edited lines out of 31 transgenic plants were generated. Deep sequencing results showed that the mutants had six different mutation types at the target site of the TVHYNP domain of the SLR1 gene. The homo-edited plants selected individuals without DNA (T-DNA) transcribed by segregation in the T1 generation. The slr1-d7 and slr1-d8 plants caused a gibberellin (GA)-insensitive dwarf phenotype with shrunken leaves and shortened internodes. A genome-wide gene expression analysis by RNA-seq indicated that the expression levels of two GA-related genes, GA20OX2 (Gibberellin oxidase) and GA3OX2, were increased in the edited mutant plants, suggesting that GA20OX2 acts as a convert of GA12 signaling. These mutant plants are required by altering GA responses, at least partially by a defect in the phytohormone signaling system process and prevented cell elongation. The new mutants, namely, the slr1-d7 and slr1-d8 lines, are valuable semi-dominant dwarf alleles with potential application value for molecule breeding using the CRISPR/Cas9 system in rice.

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