A Correction to the Review Titled: "De Novo Organ Formation from Differentiated Cells: Root Nodule Organogenesis" by M. Crespi and F. Frugier

2009 ◽  
Vol 2 (53) ◽  
pp. er1-er1
Keyword(s):  
Root Nodule ◽  
De Novo ◽  
Organ Formation ◽  
Differentiated Cells

scholarly journals Progressive methylation of POU5F1 regulatory regions during blastocyst development

Reproduction ◽  
2018 ◽  
Vol 156 (2) ◽  
pp. 145-161 ◽  
Author(s):  
E Canon ◽  
L Jouneau ◽  
T Blachère ◽  
N Peynot ◽  
N Daniel ◽  
...  
Keyword(s):  
De Novo ◽  
Regulatory Region ◽  
Upstream Region ◽  
Distal Enhancer ◽  
Blastocyst Development ◽  
Differentiated Cells ◽  
Rabbit Blastocyst ◽  
Highly Correlated ◽  
And Function

ThePOU5F1gene encodes one of the ‘core’ transcription factors necessary to establish and maintain pluripotency in mammals. Its function depends on its precise level of expression, so its transcription has to be tightly regulated. To date, few conserved functional elements have been identified in its 5′ regulatory region: a distal and a proximal enhancer, and a minimal promoter, epigenetic modifications of which interfere withPOU5F1expression and function inin vitro-derived cell lines. Also, its permanent inactivation in differentiated cells depends onde novomethylation of its promoter. However, little is known about the epigenetic regulation ofPOU5F1expression in the embryo itself. We used the rabbit blastocyst as a model to analyze the methylation dynamics of thePOU5F15′ upstream region, relative to its regulated expression in different compartments of the blastocyst over a 2-day period of development. We evidenced progressive methylation of the 5′ regulatory region and the first exon accompanying differentiation and the gradual repression ofPOU5F1. Methylation started in the early trophectoderm before complete transcriptional inactivation. Interestingly, the distal enhancer, which is known to be active in naïve pluripotent cells only, retained a very low level of methylation in primed pluripotent epiblasts and remained less methylated in differentiated compartments than the proximal enhancer. This detailed study identified CpGs with the greatest variations in methylation, as well as groups of CpGs showing a highly correlated behavior, during differentiation. Moreover, our findings evidenced few CpGs with very specific behavior during this period of development.

Abstract 193: RNA-sequencing of Disease-specific iPSC as a New Filter to Identify Genes Associated With Hypoplastic Left Heart Syndrome

2015 ◽  
Vol 117 (suppl_1) ◽  
Author(s):  
Almudena Martinez Fernandez ◽  
Xing Li ◽  
Jeanne L Theis ◽  
Andre Terzic ◽  
Timothy M Olson ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Hypoplastic Left Heart Syndrome ◽  
De Novo ◽  
Nuclear Family ◽  
Cardiac Differentiation ◽  
Left Heart ◽  
Hypoplastic Left Heart ◽  
Differentiated Cells ◽  
Left Heart Syndrome

Hypoplastic Left Heart Syndrome (HLHS) is a complex multifactorial disease for which no definitive genetic causes have been found. Current genetic filtering strategies render lists of genes with unknown relevance in terms of pathogenesis. A complementary filter based on biological evidence would create a new approach to prioritize relevant candidate genes and mutations. In our study, 5 members of a nuclear family including a child with HLHS were evaluated using echocardiography and their genetic information was obtained through whole genome sequencing (WGS). Data filtering including rarity, functional impact and mode of inheritance was implemented, resulting in identification of 34 genes with recessive or de novo variants potentially involved in the pathogenesis of HLHS. Additionally, iPSC were derived from proband and parents and subjected to RNA-sequencing at the undifferentiated state and following spontaneous differentiation. Comparative transcriptional analyses identified genes differentially expressed in proband samples at each stage. These gene sets were used as an additional filter for the previously generated WGS data. This strategy revealed that out of 34 mutated genes originally identified, 10 displayed transcriptional differences in undifferentiated iPSC from the HLHS-affected individual while 16 out of 34 mutated genes showed significantly different expression levels in differentiated cells from proband. Furthermore, expression dynamics were studied during guided cardiac differentiation for the 9 genes fulfilling all applied criteria. Two genes not previously linked to HLHS, ELF4 and HSPG2 were found to behave significantly different in HLHS-iPSC when compared to control counterparts. In summary, filtering WGS data according to a new layer of transcriptional information that leverages iPSC plasticity allows prioritization of genes associated with HLHS in an in vitro model of disease.

scholarly journals Regulation of CXCR6 Expression on Adipocytes and Osteoblasts Differentiated from Human Adipose Tissue-Derived Mesenchymal Stem Cells

2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Seung-Cheol Lee ◽  
Yoo-Jung Lee ◽  
Min Kyoung Shin ◽  
Jung-Suk Sung
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Adipose Tissue ◽  
Cell Activation ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Human Mesenchymal Stem Cells ◽  
De Novo Synthesis ◽  
Differentiation Potential ◽  
Differentiated Cells

Human mesenchymal stem cells derived from adipose tissue (hADMSCs) are a desirable candidate in regenerative medicine. hADMSCs secrete growth factors, cytokines, and chemokines and also express various receptors that are important in cell activation, differentiation, and migration to injured tissue. We showed that the expression level of chemokine receptor CXCR6 was significantly increased by ~2.5-fold in adipogenic-differentiated cells (Ad), but not in osteogenic-differentiated cells (Os) when compared with hADMSCs. However, regulation of CXCR6 expression on hADMSCs by using lentiviral particles did not affect the differentiation potential of hADMSCs. Increased expression of CXCR6 on Ad was mediated by both receptor recycling, which was in turn regulated by secretion of CXCL16, and de novo synthesis. The level of soluble CXCL16 was highly increased in both Ad and Os in particular, which inversely correlates with the expression on a transmembrane-bound form of CXCL16 that is cleaved by disintegrin and metalloproteinase. We concluded that the expression of CXCR6 is regulated by receptor degradation or recycling when it is internalized by interaction with CXCL16 and by de novo synthesis of CXCR6. Overall, our study may provide an insight into the molecular mechanisms of the CXCR6 reciprocally expressed on differentiated cells from hADMSCs.

scholarly journals Tissue-specific metabolic reprogramming during wound induced de novo organ formation in tomato hypocotyl explants

2021 ◽  
Author(s):  
Eduardo Larriba ◽  
Ana Belén Sánchez García ◽  
Cristina Martínez-Andújar ◽  
Alfonso Albacete ◽  
José Manuel Pérez-Pérez
Keyword(s):  
De Novo ◽  
Metabolic Reprogramming ◽  
Apical Region ◽  
List Type ◽  
Basal Region ◽  
Metabolic Switch ◽  
Tissue Specific ◽  
Hypocotyl Explants ◽  
Organ Formation ◽  
Organ Regeneration

SUMMARYPlants have remarkable regenerative capacity, which allows them to survive tissue damaging after biotic and abiotic stress. Some of the key transcription factors and the hormone crosstalk involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. However, little is known about the role of metabolism in wound-induced organ regeneration.Here, we performed detailed transcriptome analysis and targeted metabolomics approach during de novo organ formation in tomato hypocotyl explants and found tissue-specific metabolic differences and divergent developmental pathways after wounding.Our results indicate that callus growth in the apical region of the hypocotyl depends on a specific metabolic switch involving the upregulation of the photorespiratory pathway and the differential regulation of photosynthesis-related genes and of the gluconeogenesis pathway.The endogenous pattern of ROS accumulation in the apical and basal region of the hypocotyl during the time-course were dynamically regulated, and contributed to tissue-specific wound-induced regeneration.Our findings provide a useful resource for further investigation on the molecular mechanisms involved in wound-induced organ formation in a crop species such as tomato.One-sentence SummaryMetabolic switch during wound-induced regeneration

scholarly journals Rates of degradation and synthesis of glycosidases de novo during growth and differentiation of Dictyostelium discoideum

1975 ◽  
Vol 148 (2) ◽  
pp. 169-177 ◽  
Author(s):  
D Every ◽  
J M Ashworth
Keyword(s):  
Amino Acids ◽  
Enzyme Activity ◽  
Life Cycle ◽  
Dictyostelium Discoideum ◽  
Growth Medium ◽  
Growth Phase ◽  
Enzyme Activities ◽  
De Novo ◽  
Antibody Preparation ◽  
Differentiated Cells

1. Injection of a purified preparation of β-N-acetylglucosaminidase from the spent growth medium of myxamoebae of Dictyostelium discoideum into rabbits gave rise to an antibody preparation containing both anti-α-glucosidase and anti-β-acetylglucosaminidase activities. 2. These two activities were shown to reside in different immunoglobulin molecules and it was concluded that the β-N-acetylglucosaminidase preparation contained trace amounts of highly antigenic α-glucosidase. 3. A single precipitin band having β-N-acetylglucosaminidase activity was formed in Ouchterlony plates when this antibody preparation was tested against extracts obtained from differentiated cells or from myxamoebae grown either axenically or on bacteria. 4. The antibody preparation was used to show that both β-N-acetylglucosaminidase and α-glucosidase molecules are synthesized de novo from isotopically labelled amino acids during both the growth and differentiation phases of the life cycle and to show that neither of these proteins is significantly degraded during the growth phase or during the first 9h of differentiation. 5. The rates of accumulation of these assayable enzyme activities are thus equal to their rates of synthesis during growth and early differentiation. 6. The factors regulating cellular enzyme activity during the life cycle of D. discoideum are discussed.

scholarly journals Natural Pearls

2016 ◽  
Vol 672 ◽  
pp. 80-102 ◽  
Author(s):  
Ana Vasiliu
Keyword(s):  
Structural Changes ◽  
De Novo ◽  
Differentiated Cells ◽  
Sufficient Cause ◽  
Epithelial Cell Migration ◽  
Shell Regeneration ◽  
Pearl Formation ◽  
Shell Production ◽  
Signalling Cascade ◽  
Cell Specialization

A literature less traveled – peaking between 1900-1920 – draws on pre-classical concepts of crystal growth and a trove of field biology, to understand ectopic shell production, the natural source of pearls. By 1907, grafts from the calcifying mantle epithelium on gonads induced nacre mineralization consistently in Pinctada margaritifera, suggesting that anomalously displaced, readily specialized cells are at least a sufficient cause of natural pearl formation. Otherwise, the epithelial sacks wrapping natural nacreous pearls must specialize for nacre production independently from the shell producing mantle – an idea supported by experiments with shell regeneration, but not amenable to a method of inducing pearl formation. At the time, chasing epithelial cell migration was technically unfeasible, signalling was news, stemness was fiction. Boldly, Jameson & Rubbel [1902-1912] marshalled natural pearl nuclei and shell repairs as mineral records of cells specializing de novo into the shell’s secretory regimes. Much of this paper reenacts the historic debate on the origin of pearls: thence bold ideas connect smoothly with new work both on bone or shell. I replicate Jameson’s choice of samples and revisit his proposal to search for an “agency [other than the] shell-secreting mechanism“ acting on ”replacement cells” as the origin of pearls. Much has changed: specialized epithelial cells reportedly migrate; non-differentiated cells remain available throughout and near the calcifying mantle epithelium – both, open possibilities for natural pearl nucleation. Interest in understanding the latter now connects with results sketching the signalling cascade in cell specialization toward bone morphogenesis. Replicating Jameson’s choice of samples, I describe the more spectacular structural changes in the mineralization of pearls associated with two instances of cell specialization: toward producing one shell material – in the event of natural pearl nucleation, or switching between two in later pearl growth. Clusters of cells producing distinctly novel mineralization – nacre over fibrous-prismatic aragonite – could be singled out next to natural pearls by Jameson. The possibility has not been probed in roughly a hundred years. Natural pearl nucleation as a cellular event has never been explored.

scholarly journals Tissue-Specific Metabolic Reprogramming during Wound-Induced Organ Formation in Tomato Hypocotyl Explants

2021 ◽  
Vol 22 (18) ◽  
pp. 10112
Author(s):  
Eduardo Larriba ◽  
Ana Belén Sánchez-García ◽  
Cristina Martínez-Andújar ◽  
Alfonso Albacete ◽  
José Manuel Pérez-Pérez
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Metabolic Reprogramming ◽  
Apical Region ◽  
Crop Species ◽  
Metabolic Switch ◽  
Tissue Specific ◽  
Hypocotyl Explants ◽  
Organ Formation ◽  
Organ Regeneration

Plants have remarkable regenerative capacity, which allows them to survive tissue damage after exposure to biotic and abiotic stresses. Some of the key transcription factors and hormone crosstalk mechanisms involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. However, little is known about the role of metabolism in wound-induced organ formation. Here, we performed detailed transcriptome analysis and used a targeted metabolomics approach to study de novo organ formation in tomato hypocotyl explants and found tissue-specific metabolic differences and divergent developmental pathways. Our results indicate that successful regeneration in the apical region of the hypocotyl depends on a specific metabolic switch involving the upregulation of photorespiratory pathway components and the differential regulation of photosynthesis-related gene expression and gluconeogenesis pathway activation. These findings provide a useful resource for further investigation of the molecular mechanisms involved in wound-induced organ formation in crop species such as tomato.

scholarly journals Mapping the evolving landscape of super-enhancers during cell differentiation

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yan Kai ◽  
Bin E. Li ◽  
Ming Zhu ◽  
Grace Y. Li ◽  
Fei Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Differentiation ◽  
Target Gene ◽  
Target Genes ◽  
De Novo ◽  
Cell Types ◽  
Functional Enrichment ◽  
Target Gene Expression ◽  
Differentiated Cells ◽  
Super Enhancer

Abstract Background Super-enhancers are clusters of enhancer elements that play critical roles in the maintenance of cell identity. Current investigations on super-enhancers are centered on the established ones in static cell types. How super-enhancers are established during cell differentiation remains obscure. Results Here, by developing an unbiased approach to systematically analyze the evolving landscape of super-enhancers during cell differentiation in multiple lineages, we discover a general trend where super-enhancers emerge through three distinct temporal patterns: conserved, temporally hierarchical, and de novo. The three types of super-enhancers differ further in association patterns in target gene expression, functional enrichment, and 3D chromatin organization, suggesting they may represent distinct structural and functional subtypes. Furthermore, we dissect the enhancer repertoire within temporally hierarchical super-enhancers, and find enhancers that emerge at early and late stages are enriched with distinct transcription factors, suggesting that the temporal order of establishment of elements within super-enhancers may be directed by underlying DNA sequence. CRISPR-mediated deletion of individual enhancers in differentiated cells shows that both the early- and late-emerged enhancers are indispensable for target gene expression, while in undifferentiated cells early enhancers are involved in the regulation of target genes. Conclusions In summary, our analysis highlights the heterogeneity of the super-enhancer population and provides new insights to enhancer functions within super-enhancers.

Sign in / Sign up

Export Citation Format

Share Document