Novel circGFRα1 Promotes Self-Renewal of Female Germline Stem Cells Mediated by m6A Writer METTL14

YTHDF1's grip on CRC vasculature: insights into LINC01106 and miR-449b-5p-VEGFA axis

BACKGROUND

Investigating the unexplored territory of lncRNA m6A modification in colorectal cancer (CRC) vasculature, this study focuses on LINC01106 and YTHDF1.

METHODS

Clinical assessments reveal upregulated LINC01106 promoting vascular generation via the miR-449b-5p-VEGFA pathway.

RESULTS

YTHDF1, elevated in CRC tissues, emerges as an adverse prognostic factor. Functional experiments showcase YTHDF1's inhibitory effects on CRC cell dynamics. Mechanistically, Me-CLIP identifies m6A-modified LINC01106, validated as a YTHDF1 target through Me-RIP.

CONCLUSIONS

This study sheds light on the YTHDF1-mediated m6A modification of LINC01106, presenting it as a key player in suppressing CRC vascular generation.

The role of m6A epigenetic modifications in tumor coding and non-coding RNA processing

BACKGROUND

Epigenetic modifications of RNA significantly contribute to the regulatory processes in tumors and have, thus, received considerable attention. The m6A modification, known as N6-methyladenosine, is the predominant epigenetic alteration found in both eukaryotic mRNAs and ncRNAs.

MAIN BODY

m6A methylation modifications are dynamically reversible and are catalyzed, removed, and recognized by the complex of m6A methyltransferase (MTases), m6A demethylase, and m6A methyl recognition proteins (MRPs). Published evidence suggests that dysregulated m6A modification results in abnormal biological behavior of mature mRNA, leading to a variety of abnormal physiological processes, with profound implications for tumor development in particular.

CONCLUSION

Abnormal RNA processing due to dysregulation of m6A modification plays an important role in tumor pathogenesis and potential mechanisms of action. In this review, we comprehensively explored the mechanisms by which m6A modification regulates mRNA and ncRNA processing, focusing on their roles in tumors, and aiming to understand the important regulatory function of m6A modification, a key RNA epigenetic modification, in tumor cells, with a view to providing theoretical support for tumor diagnosis and treatment. Video Abstract.

M6A transcriptome-wide map of circRNAs identified in the testis of normal and AZ-treated Xenopus laevis

BACKGROUND

Evidence showed that N6-methyladenosine (m6A) is strongly associated with male germline development. However, the role of m6A methylation on circRNAs in amphibians remains unknown. In this study, we conducted m6A sequencing analysis to explore the m6A transcriptome-wide profile of circRNAs in testis tissues of Xenopus laevis (X. laevis) with and without treatment with 100 µg/L atrazine (AZ).

RESULTS

The analysis showed that m6A modification of circRNAs enriched in sense overlapping in testes of X. laevis. We identified the differential m6A modification sites within circRNAs in testes of AZ-exposed X. laevis and compared that with animals from control group. The results showed that a total of 1507 methylated m6A sites was induced by AZ (760 up-methylated and 747 down-methylated). The cross-analysis exhibited a negative correlation of differentially methylated m6A peaks and circRNAs expression level. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that 20 key pathways may be involved in the mechanism of testis damage of AZ-exposed X. laevis.

CONCLUSIONS

These findings indicated that differentially m6A-methylated circRNAs may play important roles in abnormal testis development of AZ-exposed X. laevis. This study is the first report about a map of m6A modification of circRNAs in male X. laevis and provides a basis for further studying on the function and mechanism of m6A methylation of circRNAs in the testis development of amphibian.

CircRNAs: versatile players and new targets in organ fibrosis

Organ fibrosis can occur in virtually all major organs with relentlessly progressive and irreversible progress, ultimately resulting in organ dysfunction and potentially death. Unfortunately, current clinical treatments cannot halt or reverse the progression of fibrosis to end-stage organ failure, and thus, advanced antifibrotic therapeutics are urgently needed. In recent years, a growing body of research has revealed that circular RNAs (circRNAs) play pivotal roles in the development and progression of organ fibrosis through highly diverse mechanisms of action. Thus, manipulating circRNAs has emerged as a promising strategy to mitigate fibrosis across different organ types. In this review, we systemically summarize the current state of knowledge about circRNA biological properties and the regulatory mechanisms of circRNAs. A comprehensive overview of major fibrotic signaling pathways and representative circRNAs that are known to modulate fibrotic signals are outlined. Then, we focus on the research progress of the versatile functional roles and underlying molecular mechanisms of circRNAs in various fibrotic diseases in different organs, including the heart, liver, lung, kidney and skin. Finally, we offer a glimpse into the prospects of circRNA-based interference and therapy, as well as their utilization as biomarkers in the diagnosis and prognosis of fibrotic diseases. Video abstract.

Mechanisms of RNA export and nuclear retention

With the identification of huge amount of noncoding RNAs in recent years, the concept of RNA localization has extended from traditional mRNA export to RNA export of mRNA and ncRNA as well as nuclear retention of ncRNA. This review aims to summarize the recent findings from studies on the mechanisms of export of different RNAs and nuclear retention of some lncRNAs in higher eukaryotes, with a focus on splicing-dependent TREX recruitment for the export of spliced mRNA and the sequence-dependent mechanism of mRNA export in the absence of splicing. In addition, evidence to support the involvement of m⁶ A modification in RNA export with the coordination between the methylase complex and TREX complex as well as sequence-dependent nuclear retention of lncRNA is recapitulated. Finally, a model of sequence-dependent RNA localization is proposed along with the many questions that remain to be answered. This article is categorized under: RNA Export and Localization > RNA Localization RNA Export and Localization > Nuclear Export/Import.

N6-methyladenosine regulator-mediated methylation modification patterns and immune infiltration characterization in Polycystic Ovary Syndrome (PCOS)

BACKGROUND

Polycystic ovary syndrome (PCOS) is a multisystem-related disease whose pathophysiology is still unclear. Several regulators of N6-methyladenosine (m6A) modification were confirmed to play a regulatory role in PCOS. Nonetheless, the roles of m6A regulators in PCOS are not fully demonstrated.

MATERIALS AND METHODS

Four mRNA expression profiling microarrays were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed m6A regulators between PCOS and normal patients were identified by R software. A random forest modal and nomogram were developed to assess the relationship between m6A regulators and the occurrence risk of PCOS. A consensus clustering method was utilized to distinctly divide PCOS patients into two m6A subtypes (m6A cluster A/B). The patterns of differential expression and immune infiltration were explored between the two m6A clusters.

RESULTS

In this study, 22 significant m6A regulators were identified between healthy controls and PCOS patients. The random forest model determined three optimal m6A regulators which are related to the occurrence risk of PCOS, including YTHDF1, RBM15 and METTL14. A nomogram was established based on these genes, and its predictive reliability was validated by decision curve analysis. The consensus clustering algorithm distinctly divided PCOS cases into two m6A subtypes. The ssGSEA algorithm found that the immune infiltration was markedly enriched in m6A cluster B than in cluster A. The m6A-pattern related differentially expressed genes (DEGs) of the two m6A subtypes were demonstrated by differential expression analysis. We found that they were enriched in immune-related genes and various infection pathways. Based on the m6A-pattern related DEGs, the PCOS patients were classified into two m6A-pattern related genomic subtypes (gene clusters A and B).

CONCLUSIONS

The present study provided evidence concerning the different modification patterns of m6A regulators in PCOS compared with normal patients. This study will help clarify the overall impact of m6A modification patterns and related immune infiltration on PCOS.

Overview of m6A and circRNAs in human cancers

N⁶-methyladenosine (m⁶A), the richest post-transcriptional modification of RNA in eukaryotic cells, is dynamically installed/uninstalled by the RNA methylase complex ("writer") and demethylase ("eraser") and recognized by the m⁶A-binding protein ("reader"). M⁶A modification on RNA metabolism involves maturation, nuclear export, translation and splicing, thereby playing a critical role in cellular pathophysiology and disease processes. Circular RNAs (circRNAs) are a class of non-coding RNAs with a covalently closed loop structure. Due to its conserved and stable properties, circRNAs could participate in physiological and pathological processes through unique pathways. Despite the recent discovery of m⁶A and circRNAs remains in the initial stage, research has shown that m⁶A modifications are widespread in circRNAs and regulates circRNA metabolism, including biogenesis, cell localization, translation, and degradation. In this review, we describe the functional crosstalk between m⁶A and circRNAs, and illustrate their roles in cancer development. Moreover, we discuss the potential mechanisms and future research directions of m⁶A modification and circRNAs.

Circular RNA ame_circ_2015 Function as microRNA Sponges in Regulating Egg-Laying of Honeybees (Apis mellifera)

Honeybees (Apis mellifera) are critical to maintaining ecological balance and are important pollinators. The oviposition behavior in honeybees is important and complex. Circular RNAs (circRNAs) are found to form circRNA-miRNA crosstalk and play important roles in reproduction processes. Here, dual luciferase reporter was used to confirm the crosstalk between ame_circ_2015 and ame_miR-14-3p. Functional experiments in vitro and in vivo were performed to investigate the biological functions of ame_circ_2015 in egg-laying of queens. The results showed that ame_circ_2015 directly target ame_miR-14-3p, and the expression of ame_circ_2015 was negatively correlated with ame_miR-14-3p expression. Overexpression results showed that ame_circ_2015 promoted the number of eggs laid and knockdown of ame_circ_2015 suppressed the number of eggs laid. It demonstrates that up-regulated ame_circ_2015 promotes the number of eggs laid by sponging ame_miR-14-3p. The study will provide information towards a better understanding of circRNA-miRNA crosstalk in egg-laying in honeybees.

N6-Methyladenosine Methylation of mRNA in Cell Senescence

Cell senescence is the growth arrest caused by the accumulation of irreparable cell damage, which is involved in physiological and pathological processes and regulated by the post-transcriptional level. This regulation is performed by transcriptional regulators and driven by aging-related small RNAs, long non-coding RNAs, and RNA-binding proteins. N6-methyladenosine (m⁶A) is the most common chemical modification in eukaryotic mRNA, which can enhance or reduce the binding of transcriptional regulators. Increasing studies have confirmed the crucial role of m⁶A in controlling mRNA in various physiological processes. Remarkably, recent reports have indicated that abnormal methylation of m⁶A-related RNA may affect cell senescence. In this review, we clarified the association between m⁶A modification and cell senescence and analyzed the limitations of the current research.

The Role of m6A on Female Reproduction and Fertility: From Gonad Development to Ovarian Aging

The growth and maturation of oocyte is accompanied by the accumulation of abundant RNAs and posttranscriptional regulation. N6-methyladenosine (m⁶A) is the most prevalent epigenetic modification in mRNA, and precisely regulates the RNA metabolism as well as gene expression in diverse physiological processes. Recent studies showed that m⁶A modification and regulators were essential for the process of ovarian development and its aberrant manifestation could result in ovarian aging. Moreover, the specific deficiency of m⁶A regulators caused oocyte maturation disorder and female infertility with defective meiotic initiation, subsequently the oocyte failed to undergo germinal vesicle breakdown and consequently lost the ability to resume meiosis by disrupting spindle organization as well as chromosome alignment. Accumulating evidence showed that dysregulated m⁶A modification contributed to ovarian diseases including polycystic ovarian syndrome (PCOS), primary ovarian insufficiency (POI), ovarian aging and other ovarian function disorders. However, the complex and subtle mechanism of m⁶A modification involved in female reproduction and fertility is still unknown. In this review, we have summarized the current findings of the RNA m⁶A modification and its regulators in ovarian life cycle and female ovarian diseases. And we also discussed the role and potential clinical application of the RNA m⁶A modification in promoting oocyte maturation and delaying the reproduction aging.

Emerging roles of circular RNAs in stem cells

Circular RNAs (circRNAs) are a novel class of noncoding RNAs that widely exist in eukaryotes. As a new focus in the field of molecular regulation, circRNAs have attracted much attention in recent years. Previous studies have confirmed that circRNAs are associated with many physiological and pathological processes. CircRNAs also participate in the regulation of stem cells. Stem cells have the properties of self-renewal and differentiation, which make stem cell therapy popular. CircRNAs may serve as new targets in stem cell therapy due to their regulation in stem cells. However, the underlying relationships between circRNAs and stem cells are still being explored. In this review, we briefly summarize the effects of circRNAs on stem cells, in the context of biological activities, aging and apoptosis, and aberrant changes. Moreover, we also examine the biological roles of stem cell-derived exosomal circRNAs. We believe our review will provide insights into the effects of circRNAs on stem cells.

Interactions of circRNAs with methylation: An important aspect of circRNA biogenesis and function (Review)

Circular RNA (circRNA) molecules are noncoding RNAs with unique circular covalently closed structures that contribute to gene expression regulation, protein translation and act as microRNA sponges. circRNAs also have important roles in human disease, particularly tumorigenesis and antitumor processes. Methylation is an epigenetic modification that regulates the expression and roles of DNA and coding RNA and their interactions, as well as of noncoding RNA molecules. Previous studies have focused on the effects of methylation modification on circRNA expression, transport, stability, translation and degradation of circRNAs, as well as how circRNA methylation occurs and the influence of circRNAs on methylation modification processes. circRNA and methylation can also regulate disease pathogenesis via these interactions. In the present study, we define the relationship between circRNAs and methylation, as well as the functions and mechanisms of their interactions during disease progression.

Novel insights into the interaction between N6-methyladenosine modification and circular RNA

As the most prevalent type of RNA modification in eukaryotes, N6-methyladenosine (m⁶A) can modulate RNA fates such as processing, splicing, maturation, export, stability, translation, and degradation. Circular RNAs (circRNAs), a novel type of non-coding RNA (ncRNAs) characterized by a covalently closed loop structure, play an essential role in various physiological and pathological processes. Extensive studies have revealed that m⁶A modification is widespread in circRNAs and influences their biogenesis and functions. Intriguingly, circRNAs can affect m⁶A modification by regulating m⁶A regulatory proteins. In this review, we summarize the characteristics and biological functions of m⁶A and circRNAs and focus on recent advances in the interaction of m⁶A modification and circRNAs. In addition, the potential clinical applications of m⁶A modification and circRNAs in diagnosis and therapeutic targets are discussed.

METTL14-mediated m6A modification of circORC5 suppresses gastric cancer progression by regulating miR-30c-2-3p/AKT1S1 axis

Background

N6-methyladenosine (m6A) RNA methylation and circular RNAs (circRNAs) have been shown to act vital roles in multiple malignancies including gastric cancer (GC). However, there is little knowledge about how m6A modification of circRNAs contributes to GC progression.

Methods

The association of METTL14 expression with the clinicopathological characteristics and prognosis in patients with GC was assessed by Western blot, Immunohistochemistry and public datasets. In vitro and vivo function experiments were conducted to investigate the role of METTL14 in GC. Furthermore, m6A-circRNA epitranscriptomic microarray was utilized to identify METTL14-mediated m6A modification of circRNAs, which were validated by methylated RNA immunoprecipitation (Me-RIP), RT-qPCR and rescue experiments in GC cells. The sponge of circORC5 with miR-30c-2-3p was confirmed by luciferase gene report and RNA immunoprecipitation assays. The expression, localization and prognosis of circORC5 in GC were evaluated by fluorescence in situ hybridization. The effects of METTL14 and (or) circORC5 on miR-30c-2-3p-mediated AKT1S1 and EIF4B were estimated by RT-qPCR and Western blot analyses.

Results

We found that METTL14 was downregulated in GC tissue samples and its low expression acted as a prognostic factor of poor survival in patients with GC. Ectopic expression of METTL14 markedly repressed growth and invasion of GC cells in vitro and in vivo, whereas knockdown of METTL14 harbored the opposite effects. Mechanically, m6A-circRNA epitranscriptomic microarray and Me-RIP identified circORC5 as the downstream target of METTL14. Silencing of METTL14 reduced the m6A level of circORC5, but increased circORC5 expression. Moreover, circORC5 could sponge miR-30c-2-3p, and reverse METTL14-caused upregulation of miR-30c-2-3p and downregulation of AKT1S1 and EIF4B. In addition, circORC5 possessed a negative correlation with miR-30c-2-3p and indicated a poor survival in GC.

Conclusion

Our findings demonstrate that METTL14-mediated m6A modification of circORC5 suppresses gastric cancer progression by regulating miR-30c-2-3p/AKT1S1 axis.

Hsa_circ_0006677 regulates special AT-rich binding protein-2-mediated tumor-suppressive effect via functioning as a miR-1245a sponge in non-small cell lung cancer

Non-small cell lung cancer (NSCLC) is still one of the most challenging malignant tumors. Deregulation of circular RNAs (circRNAs) is associated with NSCLC progression. However, the regulatory mechanism of circRNAs in NSCLC still needs to be studied. We selected a differentially expressed hsa_circ_0006677 (circ_0006677) in NSCLC through analyzing the GSE158695 and GSE112214 datasets. Expression of circ_0006677 was evaluated by real-time quantitative polymerase-chain reaction (RT-qPCR). Effects of circ_0006677 overexpression on NSCLC cell proliferation, apoptosis, migration, invasion, and stemness were determined by clonogenic, 5-ethynyl-2’-deoxyuridine (EdU), flow cytometry, transwell, and sphere formation assays. The regulatory mechanism of circ_0006677 was predicted by bioinformatics analysis and verified by dual-luciferase reporter and RIP assays. Animal experiments were carried out to validate the function of circ_0006677 in vivo. We observed the downregulation of circ_0006677 in NSCLC samples and cells. Functionally, circ_0006677 overexpression decreased xenograft tumor growth and restrained NSCLC cell proliferation, invasion, migration, stemness, and induced NSCLC cell apoptosis in vitro. Molecular mechanism experiments exhibited that circ_0006677 functioned as a miR-1245a sponge and mediated SATB2 expression through adsorbing miR-1245a. Either miR-1245a overexpression or SATB2 knockdown weakened circ_0006677 overexpression-mediated repression on proliferation, invasion, migration, and stemness. In conclusion, circ_0006677 regulated SATB2-mediated tumor-suppressive effect via acting as a miR-1245a sponge in NSCLC, providing a new mechanism for understanding the progression of NSCLC.

N6-Methyladenosine Modifications in the Female Reproductive System: Roles in Gonad Development and Diseases

N6-methyladenosine (m⁶A) is the most prevalent chemical modification in eukaryotic messenger RNAs. By participating in various RNA-related bioprocesses including RNA decay, splicing, transport and translation, m⁶A serves as a pivotal regulator of RNA fate and plays an irreplaceable role in cellular activities. The m⁶A modifications of transcripts are coordinately regulated by methyltransferase “writers” and demethylase “erasers”, and produce variable effects via different m⁶A reading protein “readers”. There is emerging evidence that m⁶A modifications play a critical role in a variety of physiological and pathological processes in the female reproductive system, subsequently affecting female fertility. Here, we introduce recent advances in research on m⁶A regulators and their functions, then highlight the role of m⁶A in gonad development and female reproductive diseases, as well as the underlying mechanisms driving these processes.

The Roles of RNA N6-Methyladenosine in Regulating Stem Cell Fate

RNA N6-methyladenosine (m⁶A) modification has important regulatory roles in determining cell fate. The reversible methylation process of adding and removing m⁶A marks is dynamically regulated by a fine-tuned coordination of many enzymes and binding proteins. Stem cells have self-renewal and pluripotent potential and show broad prospects in regenerative medicine and other fields. Stem cells have also been identified in cancer, which is linked to cancer metastasis, therapy resistance, and recurrence. Herein, we aimed to review the molecular mechanism that controls the reversible balance of m⁶A level in stem cells and the effect of m⁶A modification on the balance between pluripotency and differentiation. Additionally, we also elaborated the association between aberrant m⁶A modification and the maintenance of cancer stem cells in many cancers. Moreover, we discussed about the clinical implications of m⁶A modification in cancer stem cells for cancer diagnosis and therapy.

Crosstalk between N6-methyladenosine modification and circular RNAs: current understanding and future directions

N⁶-methyladenosine (m⁶A) is a prevalent internal modification in eukaryotic RNAs regulated by the so-called "writers", "erasers", and "readers". m⁶A has been demonstrated to exert critical molecular functions in modulating RNA maturation, localization, translation and metabolism, thus playing an essential role in cellular, developmental, and disease processes. Circular RNAs (circRNAs) are a class of non-coding RNAs with covalently closed single-stranded structures generated by back-splicing. CircRNAs also participate in physiological and pathological processes through unique mechanisms. Despite their discovery several years ago, m⁶A and circRNAs has drawn increased research interest due to advances in molecular biology techniques these years. Recently, several scholars have investigated the crosstalk between m⁶A and circRNAs. In this review, we provide an overview of the current knowledge of m⁶A and circRNAs, as well as summarize the crosstalk between these molecules based on existing research. In addition, we present some suggestions for future research perspectives.