Genome-Wide DNA Methylation Analysis During Palatal Fusion Reveals the Potential Mechanism of Enhancer Methylation Regulating Epithelial Mesenchyme Transformation

LAMA5: A new pathogenic gene for non-syndromic cleft lip with or without cleft palate

BACKGROUND

This study aimed to investigate the effect of LAMA5 on palatal development in mice.

METHODS

The palatine process of C57BL/6 J fetal mice on the embryonic day 13.5 (E13.5) was cultured in vitro via the rotating culture method. The LAMA5-shRNA adenovirus vector was constructed, then transfected into the palatal process of E13.5 for 48 h in vitro. A fluorescence microscope was used to visualize the fusion of palates. The expression of LAMA5 was also detected. The expression of ki67, cyclin D1, caspase 3, E-cadherin, vimentin and SHH signaling pathway-related signaling factors in the blank control group, the negative control group, and the LAMA5 interference group were detected after virus transfection.

RESULTS

The bilateral palates in the LAMA5 interference group were not fused after virus transfection. PCR and WB showed that the mRNA and protein expressions of LAMA5 were decreased in the LAMA5 interference group. Furthermore, the mRNA and protein expressions of ki67, cyclin D1 and gli1 were decreased in the LAMA5 interference group, while the mRNA and protein expressions of caspase 3 were increased. However, the mRNA and protein expression of E-cadherin, vimentin, Shh and ptch1 did not significantly change in the LAMA5 interference group.

CONCLUSIONS

LAMA5 silencing causes cleft palate by inhibiting the proliferation of mouse palatal cells and promoting apoptosis, which may not be involved in EMT. LAMA5 silencing can also cause cleft palate by interfering with the SHH signaling pathway.

Exposure to volatile organic compounds induces cardiovascular toxicity that may involve DNA methylation

Volatile organic compounds (VOCs) are common air pollutants and water contaminants. We previously found maternal exposure to VOCs was associated with offspring congenital heart disease (CHD). However, little information is available about the effects of VOCs on cardiovascular development at embryonic stage and the underlying mechanism remains unclear. In this study, we aimed to investigate the effects of a mixture of six VOCs on cardiovascular development in zebrafish embryos. Embryos were exposed to different concentrations of VOCs mixture (32 mg/L, 64 mg/L and 128 mg/L) for 96 h, cardiovascular abnormalities including elongated heart shape, increased distance between sinus venosus and bulbus arteriosus, slowed circulation and altered heart rate were observed in a dose- and time-dependent manner. Meanwhile, VOCs exposure increased global DNA methylation levels in embryos. Analysis identified hundreds of differentially methylated sites and the enrichment of differentially methylated sites on cardiovascular development. Two differentially methylated-associated genes involved in MAPK pathway, hgfa and ntrk1, were identified to be the potential genes mediating the effects of VOCs. By enzyme-linked immunosorbent assay, altered human serum hgf and ntrk1 levels were detected in abnormal pregnancies exposed to higher VOCs levels with fetal CHD. For the first time, our study revealed exposure to VOCs induced severe cardiovascular abnormalities in zebrafish embryos. The toxicity might result from alterations in DNA methylation and corresponding expression levels of genes involved in MAPK pathway. Our study provides important information for the risk of VOCs exposure on embryonic cardiovascular development.

RA-induced prominence-specific response resulted in distinctive regulation of Wnt and osteogenesis

Proper retinoic acid (RA) signaling is essential for normal craniofacial development. Both excessive RA and RA deficiency in early embryonic stage may lead to a variety of craniofacial malformations, for example, cleft palate, which have been investigated extensively. Dysregulated Wnt and Shh signaling were shown to underlie the pathogenesis of RA-induced craniofacial defects. In our present study, we showed a spatiotemporal-specific effect of RA signaling in regulating early development of facial prominences. Although inhibited Wnt activities was observed in E12.5/E13.5 mouse palatal shelves, early exposure of excessive RA induced Wnt signaling and Wnt-related gene expression in E11.5/E12.5 mouse embryonic frontonasal/maxillary processes. A conserved regulatory network of miR-484-Fzd5 was identified to play critical roles in RA-regulated craniofacial development using RNA-seq. In addition, subsequent osteogenic/chondrogenic differentiation were differentially regulated in discrete mouse embryonic facial prominences in response to early RA induction, demonstrated using both in vitro and in vivo analyses.

Single-cell Transcriptome Landscape of DNA Methylome Regulators Associated with Orofacial Clefts in the Mouse Dental Pulp

OBJECTIVE

Significant evidence links epigenetic processes governing the dynamics of DNA methylation and demethylation to an increased risk of syndromic and nonsyndromic cleft lip and/or cleft palate (CL/P). Previously, we characterized mesenchymal stem/stromal cells (MSCs) at different stages of osteogenic differentiation in the mouse incisor dental pulp. The main objective of this research was to characterize the transcriptional landscape of regulatory genes associated with DNA methylation and demethylation at a single-cell resolution.

DESIGN

We used single-cell RNA sequencing (scRNA-seq) data to characterize transcriptome in individual subpopulations of MSCs in the mouse incisor dental pulp.

SETTINGS

The biomedical research institution.

PATIENTS/PARTICIPANTS

This study did not include patients.

INTERVENTIONS

This study collected and analyzed data on the single-cell RNA expssion in the mouse incisor dental pulp.

MAIN OUTCOME MEASURE(S)

Molecular regulators of DNA methylation/demethylation exhibit differential transcriptional landscape in different subpopulations of osteogenic progenitor cells.

RESULTS

scRNA-seq analysis revealed that genes encoding DNA methylation and demethylation enzymes (DNA methyltransferases and members of the ten-eleven translocation family of methylcytosine dioxygenases), methyl-DNA binding domain proteins, as well as transcription factors and chromatin remodeling proteins that cooperate with DNA methylation machinery are differentially expressed within distinct subpopulations of MSCs that undergo different stages of osteogenic differentiation.

CONCLUSIONS

These findings suggest some mechanistic insights into a potential link between epigenetic alterations and multifactorial causes of CL/P phenotypes.

Role of epigenetics and miRNAs in orofacial clefts

Orofacial clefts (OFCs) have multiple etiologies and likely result from an interplay between genetic and environmental factors. Within the last decade, studies have implicated specific epigenetic modifications and noncoding RNAs as additional facets of OFC etiology. Altered gene expression through DNA methylation and histone modification offer novel insights into how specific genes contribute to distinct OFC subtypes. Epigenetics research has also provided further evidence that cleft lip only (CLO) is a cleft subtype with distinct etiology. Polymorphisms or misexpression of genes encoding microRNAs, as well as their targets, contribute to OFC risk. The ability to experimentally manipulate epigenetic changes and noncoding RNAs in animal models, such as zebrafish, Xenopus, mice, and rats, has offered novel insights into the mechanisms of various OFC subtypes. Although much remains to be understood, recent advancements in our understanding of OFC etiology may advise future strategies of research and preventive care.

Genome-wide DNA methylation analysis by MethylRad and the transcriptome profiles reveal the potential cancer-related lncRNAs in colon cancer

Colon cancer (CC) is characterized by global aberrant DNA methylation that may affect gene expression and genomic stability. A series of studies have demonstrated that DNA methylation could regulate the expressions of not only protein-coding genes but also ncRNAs. However, the regulatory role of lncRNA genes methylaton in CC remains largely unknown. In the present study, we systemically characterize the profile of DNA methylation, especially the aberrant methylation of lncRNAs genes using MethylRAD technology. A total of 132 999 CCGG/8487 CCWGG sites were identified as differentially methylated sites (DMSs), which were mainly located on the introns and intergenic elements. Moreover, 1,359 CCGG/1,052 CCWGG differentially methylated genes (DMGs) were screened. Our results demonstrated that aberrant methylation of lncRNA genes occurred most frequently, accounting for 37.5% and 44.3% in CCGG and CCWGG DMGs respectively. In addition, 963 lncRNA DMGs were co-analyzed with 1328 differentially expressed lncRNAs which were identified from TCGA database. We found that 15 lncRNAs might be CC-related lncRNAs. ZNF667-AS1 and MAFA-AS1 were down-regulated in CC, which might be silenced by hypermethylation. Besides, 13 lncRNAs were hypomethylated and up-regulated in CC. Moreover, our results validated the expression and methylation level of CC-related lncRNAs by RT-qPCR and pyrosequencing assay. In conclusion, we performed a genome-wide DNA methylation analysis by MethylRAD to acquire both CCGG and CCWGG DMSs and DMGs in CC. The results screened lncRNA DMSs as potential biomarkers and identified 15 lncRNAs as CC-related lncRNAs. This study provided novel therapy targets and valuable insights into molecular mechanism in tumorigenesis and development of CC.

Integrated analysis identifying long non-coding RNAs (lncRNAs) for competing endogenous RNAs (ceRNAs) network-regulated palatal shelf fusion in the development of mouse cleft palate

BACKGROUND

Cleft palate results from the defective palatal fusion of the medial-edge epithelium after cells undergo epithelial-mesenchymal transition, a process that involves regulation by microRNAs (miRNAs). However, in palatal shelf fusion, miRNA regulation by long non-coding RNAs (lncRNAs) when acting as competing endogenous RNAs (ceRNAs) or miRNA sponges, remains unclear.

METHODS

We systematically analyzed the correlation between lncRNAs, miRNAs, and mRNAs from RNA sequencing profiling in embryonic gestation day 14.5 (E14.5) mouse embryos from control (n=3) and all-trans retinoic acid (ATRA)-treated (n=3) mice. We then constructed a lncRNA-associated ceRNA network. The expression profiles of mRNA, lncRNA, and miRNA were verified by quantitative polymerase chain reaction (qPCR).

RESULTS

In total, 18 aberrantly expressed miRNAs, 861 mRNAs, and 583 lncRNAs were identified from palate samples of control and ATRA-treated samples. Bioinformatics data and integrative analysis identified 69 lncRNAs, 18 miRNAs, and 78 mRNAs that were aberrantly expressed, and a ceRNA network was then constructed. Finally, we identified a NONMMUT004850.2/NONMMUT024276.2-miR-741-3p/miR-465b-5p-Prkar1α ceRNA network associated with palatal shelf fusion at E14.5. The qPCR results showed that NONMMUT004850.2 (P=5E-05), NONMMUT024276.2 (P=0.0012), and Prkar1α (P=3E-05) were up-regulated, whereas miR-741-3p (P=0.006) and miR-465b-5p (P=1E-04) were down-regulated in ATRA-treated mice compared to the control samples. The qPCR results were in concordance with the RNA sequencing profiling.

CONCLUSIONS

Our study demonstrated that NONMMUT004850.2/NONMMUT024276.2-miR-741-3p/miR-465b-5p-Prkar1α could potentially serve as an important regulatory mechanism of palatal fusion in the development of the cleft palate.

Genome-wide analysis of methylation in giant pandas with cataract by methylation-dependent restriction-site associated DNA sequencing (MethylRAD)

The giant panda (Ailuropoda melanoleuca) is a native species to China. They are rare and endangered and are regarded as the 'national treasure' and 'living fossil' in China. For the time being, there are only about 2500 giant pandas in the world. Therefore, we still have to do much more efforts to protect the giant pandas. In captive wildlife, the cataract incidence of mammalian always increases with age. Currently, in China, the proportion of elderly giant pandas who suffering from cataract has reached 20%. The eye disorder thus has a strong influence on the physical health and life quality of the elderly giant pandas. To discover the genes associated with the pathogenesis of cataract in the elderly giant panda and achieve the goal of early assessment and diagnosis of cataract in giant pandas during aging, we performed whole genome methylation sequencing in 3 giant pandas with cataract and 3 healthy giant pandas using methylation-dependent restriction-site associated DNA sequencing (MethylRAD). In the present study, we obtained 3.62M reads, on average, for each sample, and identified 116 and 242 differentially methylated genes (DMGs) between the two groups under the context of CCGG and CCWGG on genome, respectively. Further KEGG and GO enrichment analyses determined a total of 110 DMGs that are involved in the biological functions associated with pathogenesis of cataract. Among them, 6 DMGs including EEA1, GARS, SLITRK4, GSTM3, CASP3, and EGLN3 have been linked with cataract in old age.

Nucleic acid methylation and orofacial morphogenesis

In this review, we highlight the current state of knowledge of the diverse roles nucleic acid methylation plays in the embryonic development of the orofacial region and how aberrant methylation may contribute to orofacial clefts. We also consider the role of methylation in the regulation of neural crest cell function as it pertains to orofacial ontogeny. Changes in DNA methylation, as a consequence of environmental effects, have been observed in the regulatory regions of several genes, potentially identifying new candidate genes for orofacial clefting and opening promising new avenues for further research. While the focus of this review is primarily on the nonsyndromic forms of orofacial clefting, syndromic forms are briefly discussed in the context of aberrant nucleic acid methylation.

Position-dependent correlation between TBX22 exon 5 methylation and palatal shelf fusion in the development of cleft palate

DNA methylation is essential for spatiotemporally-regulated gene expression in embryonic development. TBX22 (Chr X: 107667964-107688978) functioning as a transcriptional repressor affects DNA binding, sumoylation, and transcriptional repression associated with X-linked cleft palate. This study aimed to explore the relationship and potential mechanism between TBX22 exon 5 methylation and palatal shelf fusion induced by all-trans retinoic acid (ATRA). We performed DNA methylation profiling, using MethylRAD-seq, after high throughput sequencing of mouse embryos from control (n=9) and ATRA-treated (to induce cleft palate, n=9) C57BL/6J mice at embryonic gestation days(E) 13.5, 14.5 and 16.5. TBX22 exon 5 was hyper-methylated at the CpG site at E13.5 (P=0.025, log2FC=1.5) and E14.5 (P=0.011, log2FC:1.5) in ATRA-treated, whereas methylation TBX22 exon 5 at the CpG site was not significantly different at E16.5 (P=0.808, log2FC=-0.2) between control and ATRA-treated. MSP results showed a similar trend consistent with the MethylRAD-seq results. qPCR showed the change in TBX22 exon 5 expression level negatively correlated with its TBX22 exon 5 methylation level. These results indicate that changes in TBX22 exon 5 methylation might play an important regulatory role during palatal shelf fusion, and may enlighten the development of novel epigenetic biomarkers in the treatment of CP in the future.

Identification of circular RNA-associated competing endogenous RNA network in the development of cleft palate

Circular RNAs (circRNAs) serve as competing endogenous RNAs (ceRNAs) and indirectly regulate gene expression through shared microRNAs (miRNAs). However, the regulatory mechanisms of circRNA as ceRNA associated with the fusion of palatal shelves in palatogenesis are yet unclear. This study aimed to explore the potential mechanism underlying the role of circRNA as ceRNA in cleft palate (CP). First, we systematically analyzed RNA-seq and miRNA-seq data after high-throughput sequencing for embryonic palatal shelf tissues from a mouse CP model induced by maternal exposure to all-trans retinoic acid on embryonic gestation day 14.5 (E14.5). Thirty-nine circRNAs, 18 miRNAs, and 936 messenger RNAs (mRNAs) were significantly dysregulated (log₂ [fold change {FC}] > 1; P < 0.05). Thereafter, we constructed a circRNA-associated ceRNA network. Finally, we determined the circRNA_0954-miRNA-881-3p-PRKAR1α ceRNA network as a hub involved in palatogenesis. Gene Ontology analysis revealed that ceRNA-related genes were associated with facial morphogenesis and developmental gene silencing. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that ceRNA-related genes are involved in apoptosis (P < 0.05, fold enrichment >1). Quantitative reverse transcription polymerase chain reaction was performed to verify the results of ceRNA analysis. We found that the circRNA-miRNA-mRNA ceRNA network is involved in palatogenesis. The present results imply that circRNA_0954-miRNA-881-3p-PRKAR1α ceRNA network may cause dysfunctional palatal fusion and might facilitate the development of novel epigenetic biomarkers to treat CP in the future.

AMBRA1-mediated autophagy and apoptosis associated with an epithelial-mesenchymal transition in the development of cleft palate induced by all-trans retinoic acid

BACKGROUND

Autophagy and apoptosis are involved in embryogenesis. However, little is known about the regulatory mechanism of AMBRA1-mediated autophagy and apoptosis associated with epithelial-mesenchymal transition (EMT) in the development of cleft palate (CP). This study is aimed to elucidate a novel regulatory mechanism by which AMBRA1 regulates autophagy and apoptosis associated with EMT during palatal fusion.

METHODS

We performed lncRNA and mRNA co-expression profile analysis on embryonic gestation day 14.5 (E14.5) mouse embryos from control (n=3) and all-trans retinoic acid-treated (to induce cleft palate, n=3) C57BL/6J mice. Functional prediction for transcription factor (TF)-target gene relationship, which was obtained using Gene Ontology/Kyoto Encyclopedia of Genes and Genomes analyses (GO/KEGG) pathway analysis, identified the regulatory "lncRNA-TF-target gene" using the trans model.

RESULTS

The trans analysis revealed that some TFs (e.g., LEF1, SMAD4, and FOXD3) regulate lncRNA and gene expression. Finally, we identified a NONMMUT034790.2-LEF1-AMBRA1 trans-regulatory network associated with CP. Our results indicate that AMBRA1 might be a novel epigenetic biomarker in palatogenesis.

CONCLUSIONS

AMBRA1-mediated autophagy and apoptosis associated with EMT by a NONMMUT034790.2-LEF1-AMBRA1 trans-regulatory network might be an important mechanism underlying dysfunctional palatal fusion.

A novel lncRNA-mediated trans-regulatory mechanism in the development of cleft palate in mouse

BACKGROUND

Increasing evidence indicates that long non-coding RNAs (lncRNAs) play crucial regulatory roles in epithelial-mesenchymal transition (EMT). However, the regulatory mechanisms during EMT of the medial edge epithelium (MEE) remain elusive. The aim of this work is to reveal a novel lncRNA-regulated dysfunction of EMT involved in the development of cleft palate (CP).

METHODS

C57BL/6 J mice at embryonic gestation day 14.5 (n = 6, 3 case samples vs. 3 control samples) were used to establish the CP model for lncRNA-mRNA co-expression profile analysis after high-throughput sequencing. Functional predictions for the differentially expressed lncRNA-mRNA co-expression with transcription factor (TF)-target gene relationship Gene Ontology/Kyoto Encyclopedia of Genes and Genomes pathway (GO/KEGG) analyses identified the regulatory "lncRNA-TF-target gene" trans model.

RESULTS

A total of 583 differentially expressed lncRNAs and 703 differentially expressed mRNAs were identified. The results of trans analysis revealed that some TFs (LEF1, SMAD4, and FOXD3) regulate lncRNAs and gene expression. Finally, we identified the NONMMUT034790.2-LEF1-SMAD7 co-expression trans-regulatory network that might be associated with CP.

CONCLUSIONS

Our results revealed that NONMMUT034790.2 might be a novel epigenetic biomarker in CP. The integration of lncRNA modulators into trans-regulatory networks will further enhance our understanding of lncRNA functions and regulatory mechanisms during palatal fusion in ATRA-induced mouse CP.

Genome-Wide DNA Methylation Profile of Gene cis-Acting Element Methylations in All-trans Retinoic Acid-Induced Mouse Cleft Palate

DNA methylation epigenetically regulates gene expression. This study is aimed to investigate genome-wide DNA methylations involved in the regulation of palatal fusion in the all-trans retinoic acid-induced mouse cleft palate model. There were 4,718,556 differentially CCGG methylated sites and 367,504 CCWGG methylated sites for 1497 genes between case and control embryonic mouse palatal tissues. The enhancers (HDAC4 and SMAD3) and promoter (MID1) of these three genes had cis-acting element methylation. HDAC4 is localized within the CCWGG, while MID1 and SMAD3 are localized within the CCGG of the gene intron. The methylation-specific polymerase chain reaction data confirmed the MethylRAD-seq results, while the quantitative reverse transcriptase-polymerase chain reaction result showed that changes in gene expression inversely were associated with the cis-acting element methylation of the gene during retinoic acid-induced palatal fusion. The GO and KEGG data showed that these three genes could regulate cell proliferation, skeletal muscle fiber development, and development-related gene signaling or activity. The cis-acting element methylation of HDAC4, SMAD3, and MID1 may play a regulatory role during palatal fusion. Further research is needed to verify these novel epigenetic biomarkers for cleft palate.