METTL14 regulates chromatin bivalent domains in mouse embryonic stem cells

A Novel Diagnostic and Subtype Classification Model Based on RNA N6-Methyladenosine Regulators for Behçet's Uveitis

PURPOSE

To investigate the role of RNA N6-methyladenosine (m6A) regulators in the diagnosis and subtype classification of Behçet's uveitis, aiming to establish a novel predictive model and explore distinct molecular patterns for personalized therapeutic approaches.

METHODS

Data from the Gene Expression Omnibus GSE209567 dataset comprising 22 Behçet's uveitis patients and 15 controls were analyzed for m6A regulator expression. Differentially expressed genes were identified using the "limma" R package, followed by random forest (RF) and support vector machine (SVM) model construction to select critical m6A regulators. A nomogram model was developed for prediction, and consensus clustering identified distinct m6A and gene-regulating patterns. Immune cell infiltration analysis was conducted using ssGSEA, and m6A scores were computed to quantify molecular patterns.

RESULTS

Eleven m6A regulators were significantly differentially expressed. The top four candidate m6A regulators (FTO, YTHDF2, CBLL1, and METTL14) were identified to predict the risk of Behçet's uveitis. A nomogram was constructed based on the four candidate m6A regulators to visualize the association between the expression levels of the candidate with the risk of onset of Behçet's uveitis. Two distinct m6A patterns and gene patterns were identified, validated by consensus clustering. High m6A scores were associated with more severe disease stages, with differential immune cell infiltration observed between subtypes. Immune-related genes, such as LRRN3 and DAAM2, were identified as key in differentiating m6A patterns.

CONCLUSION

M6A modification plays an important role in the occurrence of uveitis. Distinct m6A patterns and gene clusters highlight their potential for early diagnosis and personalized treatment.

The Functional Diversity of Chromatin-Associated RNA Binding Proteins in Transcriptional and Post-Transcriptional Regulation

RNA-binding proteins (RBPs) are a diverse class of proteins that interact with their target RNA molecules to regulate gene expression at the transcriptional and post-transcriptional levels. RBPs contribute to almost all aspects of RNA processing with sequence-specific, structure-specific, and nonspecific binding modes. Advances in our understanding of the mechanisms of RBP-mediated regulatory networks consisting of DNAs, RNAs, and protein complexes and the association between these networks and human diseases have been made very recently. Here, we discuss the "unconventional" functions of RBPs in transcriptional regulation by focusing on the cutting-edge investigations of chromatin-associated RBPs (ChRBPs). We briefly introduce examples of how ChRBPs influence the genomic features and molecular structures at the level of transcription. In addition, we focus on the post-transcriptional functions of various RBPs that regulate the biogenesis, transportation, stability control, and translation ability of circular RNA molecules (circRNAs). Lastly, we raise several questions about the clinical significance and potential therapeutic utility of disease-relevant RBPs.

METTL14-mediated m6A RNA methylation promotes the osteogenic differentiation of pPDLSCs by regulating WNT3A

Periodontitis is a chronic inflammatory disease that leads to the loss of periodontal supporting tissue. Furthermore, human periodontal ligament stem cells (hPDLSCs) are identified as candidate cells for the regeneration of periodontal and alveolar bone tissues. N6-Methyladenosine (m6A) performs a vital role in osteoporosis and bone metabolism. However, the role and mechanism of Methyltransferase-like 14 (METTL14) in the osteogenic differentiation of PDLSCs from periodontitis sufferers (pPDLSCs) is unclear. In this research, GSE223924 database analyzed the expression of METTL14 and Wnt Family Member 3A (WNT3A) in gingival tissue samples of 10 healthy subjects, 10 patients with periodontitis and peri-implantitis. RT-qPCR and western blot detected METTL14, COL1A1, Runx2, ALP, and WNT3A mRNA level and protein level. Osteogenic differentiation was evaluated by Alizarin Red S staining and ALP activity. MeRIP and dual-luciferase reporter assays verified interaction between METTL14 and WNT3A. GSE223924 database showed METTL14 was differentially expressed in patients with periodontitis and peri-implantitis. Furthermore, our data verified that METTL14 and WNT3A expression were decreased in pPDLSCs and were upregulated by osteogenic induction. METTL14 promoted osteogenic differentiation of pPDLSCs. METTL14 regulated WNT3A mRNA expression via m6A methylation. METTL14 facilitates osteogenic differentiation of pPDLSCs via modulating WNT3A, providing a possible target for improving alveolar bone regeneration outcomes.Highlights 1. METTL14 expression was decreased in pPDLSCs 2. METTL14 knockdown negatively regulated the osteogenic differentiation of pPDLSCs 3. WNT3A mRNA was a m6A-methylated target by METTL14.

Understanding epigenetic regulation in the endometrium - lessons from mouse models with implantation defects

Endometrial function, crucial for successful embryo implantation, is significantly influenced by epigenetic regulation. This review investigates the crucial roles of DNA methylation, histone modifications, chromatin remodeling, and RNA methylation in endometrial receptivity and implantation, based on a survey of recent literature on knockout mouse models with implantation defects. These models illuminate how epigenetic disruptions contribute to implantation failure, a significant human reproductive health concern. DNA methylation and histone modifications modulate endometrial receptivity by affecting gene silencing and chromatin structure, respectively. Chromatin remodeling factors also play a critical role in endometrial dynamics, influencing gene expression. Furthermore, RNA methylation emerges as critical in implantation through transcriptional and translational control. While human studies provide limited epigenetic snapshots, mouse models with suppressed epigenetic regulators reveal direct causal links between epigenetic alterations and implantation failure. Understanding these epigenetic interactions offers potential for novel therapies addressing reproductive disorders.

METTL14 regulates proliferation and differentiation of duck myoblasts through targeting MiR-133b

The development of duck pectoral muscle has a significant impact on meat quality, and miRNA and m6A modification play key roles in this process. In the early stage, by using MeRIP-seq and miRNA-seq to analyze the pectoral muscle tissue of duck embryos at day 13 (E13), day 19 (E19), and day 27 (E27) of incubation, we found that METTL14, as a core component of the m6A methylation transferase complex, showed significant differences in expression at different developmental stages and may have an important impact on pectoral muscle development. In this study, qRT-PCR detection revealed that the expression of proliferation and differentiation marker genes CDK2, CyclinD1, MYOG and MYHC varied at different stages, with the highest m6A level at E13 and the lowest expression of METTL14 at the same stage. After constructing overexpression and interference vectors for METTL14, we found that METTL14 interference promoted the proliferation of duck embryo myoblasts and inhibited differentiation, while overexpression inhibited proliferation and accelerated differentiation. In particular, the overexpression of METTL14 increased the expression of miR-133b, whose precursor sequence contains m6A modification sites, suggesting that METTL14 may participate in the regulation of muscle development by affecting the expression of miR-133b. This study provides new insights into the molecular mechanisms of duck pectoral muscle development and offers potential molecular targets for the genetic improvement of duck pectoral muscle.

METTL14 facilitates the process of sexual reversal via m6A RNA methylation in Pelodiscus sinensis

The Chinese soft-shelled turtle (Pelodiscus sinensis, P. sinensis) demonstrates noteworthy sexual dimorphism, where the males grow more rapidly and significantly larger than females under equivalent conditions. Estradiol (E2) administration can catalyze transformation from male to pseudo-female (PF), during which m6A RNA methylation undergoes considerable alterations. Nevertheless, the function of m6A methylation, specifically, the methyltransferase 14, N6-adenosine-methyltransferase non-catalytic subunit gene (METTL14) during this sex reversal process remains unclear. Within this study, we characterized the METTL14 gene, which was predominantly expressed within the ovary and demonstrated notable expression in PF individuals. Interference of METTL14 results in altered expression of methylation-related genes, yielding elevated RSPO1 expression and diminished AMH expression. Administration of E2 and METTL14-RNAi elicits 7994 differentially expressed genes (DEGs) during sexual differentiation, and KEGG enrichment analysis highlighted that METTL14 profoundly affects embryonic development through pathways including steroid hormone biosynthesis, ovarian steroidogenesis, tryptophan metabolism, and Glycolysis/Gluconeogenesis. Gene set enrichment analysis (GSEA) indicated that METTL14-RNAi triggers reduced expression of steroid hormone biosynthesis and ovarian steroidogenesis pathways while increasing the PPAR signaling pathway. In conclusion, METTL14-RNAi results in significant up-regulation of RSPO1 and down-regulation of AMH, inducing substantial alterations in pathways associated with hormone and metabolism. These findings propose that METTL14 may play a facilitating role during E2-induced sex reversal in P. sinensis, offering a novel avenue for further exploration into all-male breeding.

Comprehensive analysis of the transcriptome-wide m6A Methylome in sheep testicular development

N6-methyladenosine (m6A) modification of RNA is a critical post-transcriptional modification, that dynamically contributes to testicular development and spermatogenesis. Nevertheless, the investigation into the role of m6A in testicular development of sheep remains insufficient. Herein, we conducted a comprehensive analysis of the m6A transcriptome landscape in the testes of F1 hybrid Southdown × Hu sheep across M0 (0 months old, newborn), M3 (3 months old, sexually immature), M6 (6 months old, sexually mature), and Y1 (1 years old, adult). By profiling the m6A signatures across the transcriptome, we observed distinct differences in m6A modification patterns during sheep testicular development. Our cross-analysis of m6A and mRNA expression revealed that the expression of 743 genes and their m6A modification were concurrent. Notably, the combined analysis of the two comparative groups, M0 vs. M6 and M0 vs. Y1, exhibited a positive correlation, with 30 candidate genes each located within the largest protein-protein interaction network. Intriguingly, eight key hub genes (VEGFA, HDAC9, ZBTB40, KDM5B, MTRR, EAPS1, TSSK3, and BMP4) were identified to be associated with the regulation of sheep testicular development and spermatogenesis. These findings contribute to a deeper understanding of the dynamic role of m6A modification in sheep testicular biology. This study to map RNA m6A modification in sheep testes at different ages, providing novel insights into m6A topology and the molecular mechanisms associated with spermatogenesis in Southdown × Hu sheep F1 hybrids and laying the foundation for further investigations of mammalian spermatogenesis.

Exercise training decreases lactylation and prevents myocardial ischemia-reperfusion injury by inhibiting YTHDF2

Exercise improves cardiac function and metabolism. Although long-term exercise leads to circulating and micro-environmental metabolic changes, the effect of exercise on protein post-translational lactylation modifications as well as its functional relevance is unclear. Here, we report that lactate can regulate cardiomyocyte changes by improving protein lactylation levels and elevating intracellular N6-methyladenosine RNA-binding protein YTHDF2. The intrinsic disorder region of YTHDF2 but not the RNA m6A-binding activity is indispensable for its regulatory function in influencing cardiomyocyte cell size changes and oxygen glucose deprivation/re-oxygenation (OGD/R)-stimulated apoptosis via upregulating Ras GTPase-activating protein-binding protein 1 (G3BP1). Downregulation of YTHDF2 is required for exercise-induced physiological cardiac hypertrophy. Moreover, myocardial YTHDF2 inhibition alleviated ischemia/reperfusion-induced acute injury and pathological remodeling. Our results here link lactate and lactylation modifications with RNA m6A reader YTHDF2 and highlight the physiological importance of this innovative post-transcriptional intrinsic regulation mechanism of cardiomyocyte responses to exercise. Decreasing lactylation or inhibiting YTHDF2/G3BP1 might represent a promising therapeutic strategy for cardiac diseases.

The m6A reader YTHDC2 regulates UVB-induced DNA damage repair and histone modification

Ultraviolet B (UVB) radiation represents a major carcinogen for the development of all skin cancer types. Mechanistically, UVB induces damage to DNA in the form of lesions, including cyclobutane pyrimidine dimers (CPDs). Disruption of the functional repair processes, such as nucleotide excision repair (NER), allows persistence of DNA damage and contributes to skin carcinogenesis. Recent work has implicated m6A RNA methylation and its regulatory proteins as having critical roles in facilitating UVB-induced DNA damage repair. However, the biological functions of the m6A reader YTHDC2 are unknown in this context. Here, we show that YTHDC2 inhibition enhances the repair of UVB-induced DNA damage. We discovered that YTHDC2 inhibition increased the expression of PTEN while it decreased the expression of the PRC2 component SUZ12 and the levels of the histone modification H3K27me3. However, none of these functions were causally linked to the improvements in DNA repair, suggesting that the mechanism utilized by YTHDC2 may be unconventional. Moreover, inhibition of the m6A writer METTL14 reversed the effect of YTHDC2 inhibition on DNA repair while inhibition of the m6A eraser FTO mimicked the effect of YTHDC2 inhibition, indicating that YTHDC2 may regulate DNA repair through the m6A pathway. Finally, compared to normal human skin, YTHDC2 expression was upregulated in human cutaneous squamous cell carcinomas (cSCC), suggesting that it may function as a tumor-promoting factor in skin cancer. Taken together, our findings demonstrate that the m6A reader YTHDC2 plays a role in regulating UVB-induced DNA damage repair and may serve as a potential biomarker in cSCC.

DNA methylation regulates RNA m6A modification through transcription factor SP1 during the development of porcine somatic cell nuclear transfer embryos

Epigenetic modifications play critical roles during somatic cell nuclear transfer (SCNT) embryo development. Whether RNA N6-methyladenosine (m6A) affects the developmental competency of SCNT embryos remains unclear. Here, we showed that porcine bone marrow mesenchymal stem cells (pBMSCs) presented higher RNA m6A levels than those of porcine embryonic fibroblasts (pEFs). SCNT embryos derived from pBMSCs had higher RNA m6A levels, cleavage, and blastocyst rates than those from pEFs. Compared with pEFs, the promoter region of METTL14 presented a hypomethylation status in pBMSCs. Mechanistically, DNA methylation regulated METTL14 expression by affecting the accessibility of transcription factor SP1 binding, highlighting the role of the DNA methylation/SP1/METTL14 pathway in donor cells. Inhibiting the DNA methylation level in donor cells increased the RNA m6A level and improved the development efficiency of SCNT embryos. Overexpression of METTL14 significantly increased the RNA m6A level in donor cells and the development efficiency of SCNT embryos, whereas knockdown of METTL14 suggested the opposite result. Moreover, we revealed that RNA m6A-regulated TOP2B mRNA stability, translation level, and DNA damage during SCNT embryo development. Collectively, our results highlight the crosstalk between RNA m6A and DNA methylation, and the crucial role of RNA m6A during nuclear reprogramming in SCNT embryo development.

Bivalent chromatin: a developmental balancing act tipped in cancer

Bivalent chromatin is defined by the co-occurrence of otherwise opposing H3K4me3 and H3K27me3 modifications and is typically located at unmethylated promoters of lowly transcribed genes. In embryonic stem cells, bivalent chromatin has been proposed to poise developmental genes for future activation, silencing or stable repression upon lineage commitment. Normally, bivalent chromatin is kept in tight balance in cells, in part through the activity of the MLL/COMPASS-like and Polycomb repressive complexes that deposit the H3K4me3 and H3K27me3 modifications, respectively, but also emerging novel regulators including DPPA2/4, QSER1, BEND3, TET1 and METTL14. In cancers, both the deregulation of existing domains and the creation of de novo bivalent states is associated with either the activation or silencing of transcriptional programmes. This may facilitate diverse aspects of cancer pathology including epithelial-to-mesenchymal plasticity, chemoresistance and immune evasion. Here, we review current methods for detecting bivalent chromatin and discuss the factors involved in the formation and fine-tuning of bivalent domains. Finally, we examine how the deregulation of chromatin bivalency in the context of cancer could facilitate and/or reflect cancer cell adaptation. We propose a model in which bivalent chromatin represents a dynamic balance between otherwise opposing states, where the underlying DNA sequence is primed for the future activation or repression. Shifting this balance in any direction disrupts the tight equilibrium and tips cells into an altered epigenetic and phenotypic space, facilitating both developmental and cancer processes.