Identification of Novel Candidate Genes Implicated in Odontogenic Potential in the Developing Mouse Tooth Germ using Transcriptome Analysis

Abstract In tooth bioengineering for replacement therapy of missing teeth, the utilized cells must possess an inductive signal-forming ability to initiate odontogenesis. This ability is called odontogenic potential. In mice, the odontogenic potential signal is known to be translocated from the epithelium to the mesenchyme at the early bud stage in the developing molar tooth germ. However, the identity of the molecular constituents of this process remains unclear. Therefore, in this study, whole transcriptome profiles of the mouse molar tooth germ epithelium and mesenchyme were investigated using the RNA sequencing (RNA-seq) technique. The analyzed transcriptomes corresponded to two developmental stages, embryonic day 11.5 (E11.5) and 14.5 (E14.5), which represent the odontogenic potential shifts. We identified differentially expressed genes (DEGs), which were specifically overexpressed in both the E11.5 epithelium and E14.5 mesenchyme, but not expressed in their respective counterparts. Of the fifty-five DEGs identified, the top three most expressed transcription factor genes (transcription factor AP-2 beta isoform 3 [TFAP2B], developing brain homeobox protein 2 [DBX2], and insulin gene enhancer protein ISL-1 [ISL1]) and three tooth development-related genes (transcription factor HES-5 [HES5], platelet-derived growth factor D precursor [PDGFD], semaphrin-3A precursor [SEMA3A]) were selected and validated by quantitative RT-PCR. Using immunofluorescence staining, the TFAP2B protein expression was found to be localized only at the E11.5 epithelium and E14.5 mesenchyme. Thus, our empirical findings in the present study may provide a new perspective into the characterization of the molecules responsible for the odontogenic potential and may have an implication in the cell-based whole tooth regeneration strategy.

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Expression, localization and synthesis of small leucine-rich proteoglycans in developing mouse molar tooth germ

European Journal of Histochemistry ◽

10.4081/ejh.2020.3092 ◽

2020 ◽

Vol 64 (1) ◽

Cited By ~ 1

Author(s):

Angammana Randilini ◽

Kaoru Fujikawa ◽

Shunichi Shibata

Keyword(s):

Organ Culture ◽

Developmental Stages ◽

Tooth Development ◽

Expression Patterns ◽

Tooth Germ ◽

Molar Tooth ◽

Cervical Region ◽

Metabolic Labeling ◽

Tooth Formation ◽

Tooth Germs

The gene expression and protein synthesis of small leucine-rich proteoglycans (SLRPs), including decorin, biglycan, fibromodulin, and lumican, was analyzed in the context of the hypothesis that they are closely related to tooth formation. In situ hybridization, immunohistochemistry, and organ culture with metabolic labeling of [35S] were carried out in mouse first molar tooth germs of different developmental stages using ICR mice at embryonic day (E) 13.5 to postnatal day (P) 7.0. At the bud and cap stage, decorin mRNA was expressed only in the surrounding mesenchyme, but not within the tooth germ. Biglycan mRNA was then expressed in the condensing mesenchyme and the dental papilla of the tooth germ. At the apposition stage (late bell stage), both decorin and biglycan mRNA were expressed in odontoblasts, resulting in a switch of the pattern of expression within the different stages of odontoblast differentiation. Decorin mRNA was expressed earlier in newly differentiating odontoblasts than biglycan. With odontoblast maturation and dentin formation, decorin mRNA expression was diminished and localized to the newly differentiating odontoblasts at the cervical region. Simultaneously, biglycan mRNA took over and extended its expression throughout the new and mature odontoblasts. Both mRNAs were expressed in the dental pulp underlying the respective odontoblasts. At P7.0, both mRNAs were weakly expressed but maintained their spatial expression patterns. Immunostaining showed that biglycan was localized in the dental papillae and pulp. In addition, all four SLRPs showed clear immunostaining in predentin, although the expressions of fibromodulin and lumican mRNAs were not identified in the tooth germs examined. The organ culture data obtained supported the histological findings that biglycan is more predominant than decorin at the apposition stage. These results were used to identify biglycan as the principal molecule among the SLRPs investigated. Our findings indicate that decorin and biglycan show spatial and temporal differential expressions and play their own tissue-specific roles in tooth development.

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Seed Genome Hypomethylated Regions Are Enriched In Transcription Factor Genes

10.1101/356501 ◽

2018 ◽

Author(s):

Min Chen ◽

Jer-Young Lin ◽

Jungim Hur ◽

Julie M. Pelletier ◽

Russell Baden ◽

...

Keyword(s):

Dna Methylation ◽

Transcription Factor ◽

Seed Development ◽

Mammalian Cells ◽

Fatty Acid Biosynthesis ◽

Developmental Stages ◽

Storage Proteins ◽

Seed Formation ◽

Epigenetic Events ◽

Transcription Factor Genes

AbstractThe precise mechanisms that control gene activity during seed development remain largely unknown. Previously, we showed that several genes essential for seed development, including those encoding storage proteins, fatty acid biosynthesis enzymes, and transcriptional regulators, such as ABI3 and FUS3, are located within hypomethylated regions of the soybean genome. These hypomethylated regions are similar to the DNA methylation valleys (DMVs), or canyons, found in mammalian cells. Here, we address the question of the extent to which DMVs are present within seed genomes, and what role they might play in seed development. We scanned soybean and Arabidopsis seed genomes from post-fertilization through dormancy and germination for regions that contain < 5% or < 0.4% bulk methylation in CG-, CHG-, and CHH-contexts over all developmental stages. We found that DMVs represent extensive portions of seed genomes, range in size from 5 to 76 kb, are scattered throughout all chromosomes, and are hypomethylated throughout the plant life cycle. Significantly, DMVs are enriched greatly in transcription factor genes, and other developmental genes, that play critical roles in seed formation. Many DMV genes are regulated with respect to seed stage, region, and tissue - and contain H3K4me3, H3K27me3, or bivalent marks that fluctuate during development. Our results indicate that DMVs are a unique regulatory feature of both plant and animal genomes, and that a large number of seed genes are regulated in the absence of methylation changes during development - probably by the action of specific transcription factors and epigenetic events at the chromatin level.SignificanceWe scanned soybean and Arabidopsis seed genomes for hypomethylated regions, or DNA Methylation Valleys (DMVs), present in mammalian cells. A significant fraction of seed genomes contain DMV regions that have < 5% bulk DNA methylation, or, in many cases, no detectable DNA methylation. Methylation levels of seed DMVs do not vary detectably during seed development with respect to time, region, and tissue, and are present prior to fertilization. Seed DMVs are enriched in transcription factor genes and other genes critical for seed development, and are also decorated with histone marks that fluctuate with developmental stage, resembling in significant ways their animal counterparts. We conclude that many genes playing important roles in seed formation are regulated in the absence of detectable DNA methylation events, and suggest that selective action of transcriptional activators and repressors, as well as chromatin epigenetic events play important roles in making a seed - particularly embryo formation.

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Identification of the Novel Tooth-Specific Transcription Factor AmeloD

Journal of Dental Research ◽

10.1177/0022034518808254 ◽

2018 ◽

Vol 98 (2) ◽

pp. 234-241 ◽

Cited By ~ 7

Author(s):

B. He ◽

Y. Chiba ◽

H. Li ◽

S. de Vega ◽

K. Tanaka ◽

...

Keyword(s):

Transcription Factor ◽

Epithelial Cell ◽

Tooth Development ◽

Tooth Germ ◽

Regulatory Elements ◽

Proximal Promoter ◽

Epithelial Cell Line ◽

Bhlh Transcription Factor ◽

Specific Cell ◽

E Cadherin

Basic-helix-loop-helix (bHLH) transcription factors play an important role in various organs’ development; however, a tooth-specific bHLH factor has not been reported. In this study, we identified a novel tooth-specific bHLH transcription factor, which we named AmeloD, by screening a tooth germ complementary DNA (cDNA) library using a yeast 2-hybrid system. AmeloD was mapped onto the mouse chromosome 1q32. Phylogenetic analysis showed that AmeloD belongs to the achaete-scute complex-like ( ASCL) gene family and is a homologue of ASCL5. AmeloD was uniquely expressed in the inner enamel epithelium (IEE), but its expression was suppressed after IEE cell differentiation into ameloblasts. Furthermore, AmeloD expression showed an inverse expression pattern with the epithelial cell-specific cell–cell adhesion molecule E-cadherin in the dental epithelium. Overexpression of AmeloD in dental epithelial cell line CLDE cells resulted in E-cadherin suppression. We found that AmeloD bound to E-box cis-regulatory elements in the proximal promoter region of the E-cadherin gene. These results reveal that AmeloD functions as a suppressor of E-cadherin transcription in IEE cells. Our study demonstrated that AmeloD is a novel tooth-specific bHLH transcription factor that may regulate tooth development through the suppression of E-cadherin in IEE cells.

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Seed genome hypomethylated regions are enriched in transcription factor genes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1811017115 ◽

2018 ◽

Vol 115 (35) ◽

pp. E8315-E8322 ◽

Cited By ~ 4

Author(s):

Min Chen ◽

Jer-Young Lin ◽

Jungim Hur ◽

Julie M. Pelletier ◽

Russell Baden ◽

...

Keyword(s):

Transcription Factor ◽

Seed Development ◽

Mammalian Cells ◽

Fatty Acid Biosynthesis ◽

Developmental Stages ◽

Storage Proteins ◽

Seed Formation ◽

Epigenetic Events ◽

Transcription Factor Genes ◽

Plant Life Cycle

The precise mechanisms that control gene activity during seed development remain largely unknown. Previously, we showed that several genes essential for seed development, including those encoding storage proteins, fatty acid biosynthesis enzymes, and transcriptional regulators (e.g., ABI3, FUS3) are located within hypomethylated regions of the soybean genome. These hypomethylated regions are similar to the DNA methylation valleys (DMVs), or canyons, found in mammalian cells. Here, we address the question of the extent to which DMVs are present within seed genomes and what role they might play in seed development. We scanned soybean and Arabidopsis seed genomes from postfertilization through dormancy and germination for regions that contain <5% or <0.4% bulk methylation in CG, CHG, and CHH contexts over all developmental stages. We found that DMVs represent extensive portions of seed genomes, range in size from 5–76 kb, are scattered throughout all chromosomes, and are hypomethylated throughout the plant life cycle. Significantly, DMVs are enriched greatly in transcription factor (TF) genes and other developmental genes that play critical roles in seed formation. Many DMV genes are regulated with respect to seed stage, region, and tissue, and contain H3K4me3, H3K27me3, or bivalent marks that fluctuate during development. Our results indicate that DMVs are a unique regulatory feature of both plant and animal genomes, and that a large number of seed genes are regulated in the absence of methylation changes during development, probably by the action of specific TFs and epigenetic events at the chromatin level.

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Faculty of 1000 evaluation for An Arabidopsis mutation in translation elongation factor 2 causes superinduction of CBF/DREB1 transcription factor genes but blocks the induction of their downstream targets under low temperatures.

F1000 - Post-publication peer review of the biomedical literature ◽

10.3410/f.1006316.78957 ◽

2002 ◽

Author(s):

Michael Thomashow

Keyword(s):

Transcription Factor ◽

Low Temperatures ◽

Elongation Factor ◽

Translation Elongation Factor ◽

Translation Elongation ◽

Downstream Targets ◽

Elongation Factor 2 ◽

Transcription Factor Genes

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Faculty Opinions recommendation of Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1119.458606 ◽

2005 ◽

Author(s):

Andrew Arnold

Keyword(s):

Prostate Cancer ◽

Transcription Factor ◽

Transcription Factor Genes ◽

Ets Transcription Factor

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Expression and Co-expression Analyses of WRKY, MYB, bHLH and bZIP Transcription Factor Genes in Potato (Solanum tuberosum) Under Abiotic Stress Conditions: RNA-seq Data Analysis

Potato Research ◽

10.1007/s11540-021-09502-3 ◽

2021 ◽

Author(s):

Ertugrul Filiz ◽

Firat Kurt

Keyword(s):

Transcription Factor ◽

Abiotic Stress ◽

Solanum Tuberosum ◽

Data Analysis ◽

Stress Conditions ◽

Bzip Transcription Factor ◽

Rna Seq ◽

Transcription Factor Genes

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Identification of Transcription Factor Genes and Their Correlation with the High Diversity of Stramenopiles

PLoS ONE ◽

10.1371/journal.pone.0111841 ◽

2014 ◽

Vol 9 (11) ◽

pp. e111841 ◽

Cited By ~ 6

Author(s):

Francisco Javier Buitrago-Flórez ◽

Silvia Restrepo ◽

Diego Mauricio Riaño-Pachón

Keyword(s):

Transcription Factor ◽

Transcription Factor Genes ◽

High Diversity

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BMP Activity Is Required for Tooth Development from the Lamina to Bud Stage

Journal of Dental Research ◽

10.1177/0022034512448660 ◽

2012 ◽

Vol 91 (7) ◽

pp. 690-695 ◽

Cited By ~ 40

Author(s):

Y. Wang ◽

L. Li ◽

Y. Zheng ◽

G. Yuan ◽

G. Yang ◽

...

Keyword(s):

Cell Proliferation ◽

Molecular Marker ◽

Tooth Development ◽

Tooth Germ ◽

Bmp Signaling ◽

Expression Of Genes ◽

Dental Epithelium ◽

Initiation Stage ◽

Transgenic Embryos ◽

Bmp Antagonist

Several Bmp genes are expressed in the developing mouse tooth germ from the initiation to the late-differentiation stages, and play pivotal roles in multiple steps of tooth development. In this study, we investigated the requirement of BMP activity in early tooth development by transgenic overexpression of the extracellular BMP antagonist Noggin. We show that overexpression of Noggin in the dental epithelium at the tooth initiation stage arrests tooth development at the lamina/early-bud stage. This phenotype is coupled with a significantly reduced level of cell proliferation rate and a down-regulation of Cyclin-D1 expression, specifically in the dental epithelium. Despite unaltered expression of genes known to be implicated in early tooth development in the dental mesenchyme and dental epithelium of transgenic embryos, the expression of Pitx2, a molecular marker for the dental epithelium, became down-regulated, suggesting the loss of odontogenic fate in the transgenic dental epithelium. Our results reveal a novel role for BMP signaling in the progression of tooth development from the lamina stage to the bud stage by regulating cell proliferation and by maintaining odontogenic fate of the dental epithelium.

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