Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase

RNA m6A modification and its function in diseases

N⁶-methyladenosine (m⁶A) is the most common post-transcriptional RNA modification throughout the transcriptome, affecting fundamental aspects of RNA metabolism. m⁶A modification could be installed by m⁶A "writers" composed of core catalytic components (METTL3/METTL14/WTAP) and newly defined regulators and removed by m⁶A "erasers" (FTO and ALKBH5). The function of m⁶A is executed by m⁶A "readers" that bind to m⁶A directly (YTH domain-containing proteins, eIF3 and IGF2BPs) or indirectly (HNRNPA2B1). In the past few years, advances in m⁶A modulators ("writers," "erasers," and "readers") have remarkably renewed our understanding of the function and regulation of m⁶A in different cells under normal or disease conditions. However, the mechanism and the regulatory network of m⁶A are still largely unknown. Moreover, investigations of the m⁶A physiological roles in human diseases are limited. In this review, we summarize the recent advances in m⁶A research and highlight the functional relevance and importance of m⁶A modification in in vitro cell lines, in physiological contexts, and in cancers.

N6-Methyladenosine Role in Acute Myeloid Leukaemia

We are currently assisting in the explosion of epitranscriptomics, which studies the functional role of chemical modifications into RNA molecules. Among more than 100 RNA modifications, the N6-methyladenosine (m⁶A), in particular, has attracted the interest of researchers all around the world. m⁶A is the most abundant internal chemical modification in mRNA, and it can control any aspect of mRNA post-transcriptional regulation. m⁶A is installed by “writers”, removed by “erasers”, and recognized by “readers”; thus, it can be compared to the reversible and dynamic epigenetic modifications in histones and DNA. Given its fundamental role in determining the way mRNAs are expressed, it comes as no surprise that alterations to m⁶A modifications have a deep impact in cell differentiation, normal development and human diseases. Here, we review the proteins involved in m⁶A modification in mammals, m⁶A role in gene expression and its contribution to cancer development. In particular, we will focus on acute myeloid leukaemia (AML), which provides an initial indication of how alteration in m⁶A modification can disrupt normal cellular differentiation and lead to cancer.

Imbalance learning for the prediction of N6-Methylation sites in mRNAs

Background

N⁶-methyladenosine (m⁶A) is an important epigenetic modification which plays various roles in mRNA metabolism and embryogenesis directly related to human diseases. To identify m⁶A in a large scale, machine learning methods have been developed to make predictions on m⁶A sites. However, there are two main drawbacks of these methods. The first is the inadequate learning of the imbalanced m⁶A samples which are much less than the non-m⁶A samples, by their balanced learning approaches. Second, the features used by these methods are not outstanding to represent m⁶A sequence characteristics.

Results

We propose to use cost-sensitive learning ideas to resolve the imbalance data issues in the human mRNA m⁶A prediction problem. This cost-sensitive approach applies to the entire imbalanced dataset, without random equal-size selection of negative samples, for an adequate learning. Along with site location and entropy features, top-ranked positions with the highest single nucleotide polymorphism specificity in the window sequences are taken as new features in our imbalance learning. On an independent dataset, our overall prediction performance is much superior to the existing predictors. Our method shows stronger robustness against the imbalance changes in the tests on 9 datasets whose imbalance ratios range from 1:1 to 9:1. Our method also outperforms the existing predictors on 1226 individual transcripts. It is found that the new types of features are indeed of high significance in the m⁶A prediction. The case studies on gene c-Jun and CBFB demonstrate the detailed prediction capacity to improve the prediction performance.

Conclusion

The proposed cost-sensitive model and the new features are useful in human mRNA m⁶A prediction. Our method achieves better correctness and robustness than the existing predictors in independent test and case studies. The results suggest that imbalance learning is promising to improve the performance of m⁶A prediction.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4928-y) contains supplementary material, which is available to authorized users.

The m6A-epitranscriptomic signature in neurobiology: from neurodevelopment to brain plasticity

Research over the past decade has provided strong support for the importance of various epigenetic mechanisms, including DNA and histone modifications in regulating activity-dependent gene expression in the mammalian central nervous system. More recently, the emerging field of epitranscriptomics revealed an equally important role of post-transcriptional RNA modifications in shaping the transcriptomic landscape of the brain. This review will focus on the methylation of the adenosine base at the N6 position, termed N⁶ methyladenosine (m6A), which is the most abundant internal modification that decorates eukaryotic messenger RNAs. Given its prevalence and dynamic regulation in the adult brain, the m6A-epitranscriptome provides an additional layer of regulation on RNA that can be controlled in a context- and stimulus-dependent manner. Conceptually, m6A serves as a molecular switch that regulates various aspects of RNA function, including splicing, stability, localization, or translational control. The versatility of m6A function is typically determined through interaction or disengagement with specific classes of m6A-interacting proteins. Here we review recent advances in the field and provide insights into the roles of m6A in regulating brain function, from development to synaptic plasticity, learning, and memory. We also discuss how aberrant m6A signaling may contribute to neurodevelopmental and neuropsychiatric disorders.

The RNA Methyltransferase Complex of WTAP, METTL3, and METTL14 Regulates Mitotic Clonal Expansion in Adipogenesis

Adipocyte differentiation is regulated by various mechanisms, of which mitotic clonal expansion (MCE) is a key step. Although this process is known to be regulated by cell cycle modulators, the precise mechanism remains unclear.

Adipocyte differentiation is regulated by various mechanisms, of which mitotic clonal expansion (MCE) is a key step. Although this process is known to be regulated by cell cycle modulators, the precise mechanism remains unclear. N⁶-Methyladenosine (m⁶A) posttranscriptional RNA modification, whose methylation and demethylation are performed by respective enzyme molecules, has recently been suggested to be involved in the regulation of adipogenesis. Here, we show that an RNA N⁶-adenosine methyltransferase complex consisting of Wilms' tumor 1-associating protein (WTAP), methyltransferase like 3 (METTL3), and METTL14 positively controls adipogenesis by promoting cell cycle transition in MCE during adipogenesis. WTAP, coupled with METTL3 and METTL14, is increased and distributed in nucleus by the induction of adipogenesis dependently on RNA in vitro. Knockdown of each of these three proteins leads to cell cycle arrest and impaired adipogenesis associated with suppression of cyclin A2 upregulation during MCE, whose knockdown also impairs adipogenesis. Consistent with this, Wtap heterozygous knockout mice are protected from diet-induced obesity with smaller size and number of adipocytes, leading to improved insulin sensitivity. These data provide a mechanism for adipogenesis through the WTAP-METTL3-METTL14 complex and a potential strategy for treatment of obesity and associated disorders.

N6-methyladenosine contributes to cellular phenotype in a genetically-defined model of breast cancer progression

The mRNA modification N⁶-methyladenosine (m6A) is involved in many post-transcriptional regulatory processes including mRNA stability and translational efficiency. However, it is also imperative to correlate these processes with phenotypic outputs during cancer progression. Here we report that m6A levels are significantly decreased in genetically-defined immortalized and oncogenically-transformed human mammary epithelial cells (HMECs), as compared with their primary cell predecessor. Furthermore, the m6A methyltransferase (METTL3) is decreased and the demethylase (ALKBH5) is increased in the immortalized and transformed cell lines, providing a possible mechanism for this basal change in m6A levels. Although the immortalized and transformed cells showed lower m6A levels than their primary parental cell line, overexpression of METTL3 and METTL14, or ALKBH5 knockdown to increase m6A levels in transformed cells increased proliferation and migration. Remarkably, these treatments had little effect on the immortalized cells. Together, these results suggest that m6A modification may be downregulated in immortalized cells as a brake against malignant progression. Finally, we found that m6A levels in the immortalized and transformed cells increased in response to hypoxia without corresponding changes in METTL3, METTL14 or ALKBH5 expression, suggesting a novel pathway for regulation of m6A levels under stress.

The dual role of N6-methyladenosine modification of RNAs is involved in human cancers

As the most abundant and reversible RNA modification in eukaryotic cells, m⁶A triggers a new layer of epi‐transcription. M⁶A modification occurs through a methylation process modified by “writers” complexes, reversed by “erasers”, and exerts its role depending on various “readers”. Emerging evidence shows that there is a strong association between m⁶A and human diseases, especially cancers. Herein, we review bi‐aspects of m⁶A in regulating cancers mediated by the m⁶A‐associated proteins, which exert vital and specific roles in the development of various cancers. Generally, the m⁶A modification performs promotion or inhibition functions (dual role) in tumorigenesis and progression of various cancers, which suggests a new concept in cancer regulations. In addition, m⁶A‐targeted therapies including competitive antagonists of m⁶A‐associated proteins may provide a new tumour intervention in the future.

METTL3 regulates WTAP protein homeostasis

The Wilms tumor 1 (WT1)-associated protein (WTAP) is upregulated in many tumors, including, acute myeloid leukemia (AML), where it plays an oncogenic role by interacting with different proteins involved in RNA processing and cell proliferation. In addition, WTAP is also a regulator of the nuclear complex required for the deposition of N⁶-methyladenosine (m6A) into mRNAs, containing the METTL3 methyltransferase. However, it is not clear if WTAP may have m6A-independent regulatory functions that might contribute to its oncogenic role. Here, we show that both knockdown and overexpression of METTL3 protein results in WTAP protein upregulation, indicating that METTL3 levels are critical for WTAP protein homeostasis. However, we show that WTAP upregulation is not sufficient to promote cell proliferation in the absence of a functional METTL3. Therein, these data indicate that the reported oncogenic function of WTAP is strictly connected to a functional m6A methylation complex.

Methylation of RNA N6-methyladenosine in modulation of cytokine responses and tumorigenesis

Among myriads of distinct chemical modification in RNAs, the dynamic, reversible and fine-tuned methylation of N⁶-methyladenosine (m⁶A) is the most prevalent modification in eukaryotic mRNAs. This RNA mark is generated by proteins that act as m⁶A writers and can be reversed by proteins that act as m⁶A erasers. The RNA m⁶A modification is also mediated by another group of proteins capable of recognizing m⁶A that act as m⁶A readers. The m⁶A modification exerts direct control over the RNA metabolism including mRNA processing, mRNA exporting, translation initiation, mRNA stability and the biogenesis of long-non-coding RNA (LncRNA), thereby can influence various aspects of cell function. Evidently, m⁶A is intimately associated with cancer development and progression such as self-renewal capacity of cancer stem cells, proliferation, apoptosis and therapeutic resistance, and immune response. In this review, we will discuss the regulation and function of m⁶A, the various functions ascribed to these proteins and the emerging concepts that impact our knowledge of these proteins and their roles in the epitranscriptome. Conceivably, m⁶A may play pivotal roles in cytokine and immune response and carcinogenesis.

Link Between m6A Modification and Cancers

N6-methyladenosine (m6A) epitranscriptional modification has recently gained much attention. Through the development of m6A sequencing, the molecular mechanism and importance of m6A have been revealed. m6A is the most abundant internal modification in higher eukaryotic mRNAs, which plays crucial roles in mRNA metabolism and multiple biological processes. In this review, we introduce the characteristics of m6A regulators, including “writers” that create m6A mark, “erasers” that show demethylation activity and “readers” that decode m6A modification to govern the fate of modified transcripts. Moreover, we highlight the roles of m6A modification in several common cancers, including solid and non-solid tumors. The regulators of m6A exert enormous functions in cancer development, such as proliferation, migration and invasion. Especially, with the underlying mechanisms being uncovered, m6A and its regulators are expected to be the targets for the diagnosis and treatment of cancers.

N6-Methyladenine DNA Modification in the Human Genome

DNA N⁶-methyladenine (6mA) modification is the most prevalent DNA modification in prokaryotes, but whether it exists in human cells and whether it plays a role in human diseases remain enigmatic. Here, we showed that 6mA is extensively present in the human genome, and we cataloged 881,240 6mA sites accounting for ∼0.051% of the total adenines. [G/C]AGG[C/T] was the most significantly associated motif with 6mA modification. 6mA sites were enriched in the coding regions and mark actively transcribed genes in human cells. DNA 6mA and N⁶-demethyladenine modification in the human genome were mediated by methyltransferase N6AMT1 and demethylase ALKBH1, respectively. The abundance of 6mA was significantly lower in cancers, accompanied by decreased N6AMT1 and increased ALKBH1 levels, and downregulation of 6mA modification levels promoted tumorigenesis. Collectively, our results demonstrate that DNA 6mA modification is extensively present in human cells and the decrease of genomic DNA 6mA promotes human tumorigenesis.

RNA epitranscriptomics: Regulation of infection of RNA and DNA viruses by N6 -methyladenosine (m6 A)

N⁶ -methyladenosine (m⁶ A) was discovered 4 decades ago. However, the functions of m⁶ A and the cellular machinery that regulates its changes have just been revealed in the last few years. m⁶ A is an abundant internal mRNA modification on cellular RNA and is implicated in diverse cellular functions. Recent works have demonstrated the presence of m⁶ A in the genomes of RNA viruses and transcripts of a DNA virus with either a proviral or antiviral role. Here, we first summarize what is known about the m⁶ A "writers," "erasers," "readers," and "antireaders" as well as the role of m⁶ A in mRNA metabolism. We then review how the replications of numerous viruses are enhanced and restricted by m⁶ A with emphasis on the oncogenic DNA virus, Kaposi sarcoma-associated herpesvirus (KSHV), whose m⁶ A epitranscriptome was recently mapped. In the context of KSHV, m⁶ A and the reader protein YTHDF2 acts as an antiviral mechanism during viral lytic replication. During viral latency, KSHV alters m⁶ A on genes that are implicated in cellular transformation and viral latency. Lastly, we discuss future studies that are important to further delineate the functions of m⁶ A in KSHV latent and lytic replication and KSHV-induced oncogenesis.

m6A RNA Degradation Products Are Catabolized by an Evolutionarily Conserved N6-Methyl-AMP Deaminase in Plant and Mammalian Cells

N⁶-methylated adenine (m⁶A) is the most frequent posttranscriptional modification in eukaryotic mRNA. Turnover of RNA generates N⁶-methylated AMP (N⁶-mAMP), which has an unclear metabolic fate. We show that Arabidopsis thaliana and human cells require an N⁶-mAMP deaminase (ADAL, renamed MAPDA) to catabolize N⁶-mAMP to inosine monophosphate in vivo by hydrolytically removing the aminomethyl group. A phylogenetic, structural, and biochemical analysis revealed that many fungi partially or fully lack MAPDA, which coincides with a minor role of N⁶A-RNA methylation in these organisms. MAPDA likely protects RNA from m⁶A misincorporation. This is required because eukaryotic RNA polymerase can use N⁶-mATP as a substrate. Upon abrogation of MAPDA, root growth is slightly reduced, and the N⁶-methyladenosine, N⁶-mAMP, and N⁶-mATP concentrations are increased in Arabidopsis. Although this will potentially lead to m⁶A misincorporation into RNA, we show that the frequency is too low to be reliably detected in vivo. Since N⁶-mAMP was severalfold more abundant than N⁶-mATP in MAPDA mutants, we speculate that additional molecular filters suppress the generation of N⁶-mATP. Enzyme kinetic data indicate that adenylate kinases represent such filters being highly selective for AMP versus N⁶-mAMP phosphorylation. We conclude that a multilayer molecular protection system is in place preventing N⁶-mAMP accumulation and salvage.

RNA methylation in nuclear pre-mRNA processing

Eukaryotic RNA can carry more than 100 different types of chemical modifications. Early studies have been focused on modifications of highly abundant RNA, such as ribosomal RNA and transfer RNA, but recent technical advances have made it possible to also study messenger RNA (mRNA). Subsequently, mRNA modifications, namely methylation, have emerged as key players in eukaryotic gene expression regulation. The most abundant and widely studied internal mRNA modification is N⁶‐methyladenosine (m⁶A), but the list of mRNA chemical modifications continues to grow as fast as interest in this field. Over the past decade, transcriptome‐wide studies combined with advanced biochemistry and the discovery of methylation writers, readers, and erasers revealed roles for mRNA methylation in the regulation of nearly every aspect of the mRNA life cycle and in diverse cellular, developmental, and disease processes. Although large parts of mRNA function are linked to its cytoplasmic stability and regulation of its translation, a number of studies have begun to provide evidence for methylation‐regulated nuclear processes. In this review, we summarize the recent advances in RNA methylation research and highlight how these new findings have contributed to our understanding of methylation‐dependent RNA processing in the nucleus.

This article is categorized under:

RNA Processing > RNA Editing and Modification

RNA Processing > Splicing Regulation/Alternative Splicing

RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications

Structural basis for eukaryotic mRNA modification

All messenger RNAs in eukaryotes are modified co-transcriptionally and post-transcriptionally. They are all capped at the 5'-end and polyadenylated at the 3'-end. However, many mRNAs are also found to be chemically modified internally for regulation of mRNA processing, translation, stability, and to recode the message. This review will briefly summarize the structural basis for formation of the two most common modifications found at internal sites in mRNAs; methylation and deamination. The structures of the enzymes that catalyze these modifications show structural similarity to other family members within each modifying enzyme class. RNA methyltransferases, including METTL3/METTL14 responsible for N⁶-methyladensosine (m⁶A) formation, share a common structural core and utilize S-adenosyl methionine as a methyl donor. RNA deaminases, including adenosine deaminases acting on RNA (ADARs), also share a common structural core and similar signature sequence motif with conserved residues used for binding zinc and catalyzing the deamination reaction. In spite of recent reports of high resolution structures for members of these two RNA-modifying enzyme families, a great deal remains to be uncovered for a complete understanding of the structural basis for mRNA modification. Of particular interest is the definition of factors that control modification site specificity.

Enhancing Epitranscriptome Module Detection from m6A-Seq Data Using Threshold-Based Measurement Weighting Strategy

To date, with well over 100 different types of RNA modifications associated with various molecular functions identified on diverse types of RNA molecules, the epitranscriptome has emerged to be an important layer for gene expression regulation. It is of crucial importance and increasing interest to understand how the epitranscriptome is regulated to facilitate different biological functions from a global perspective, which may be carried forward by finding biologically meaningful epitranscriptome modules that respond to upstream epitranscriptome regulators and lead to downstream biological functions; however, due to the intrinsic properties of RNA molecules, RNA modifications, and relevant sequencing technique, the epitranscriptome profiled from high-throughput sequencing approaches often suffers from various artifacts, jeopardizing the effectiveness of epitranscriptome modules identification when using conventional approaches. To solve this problem, we developed a convenient measurement weighting strategy, which can largely tolerate the artifacts of high-throughput sequencing data. We demonstrated on real data that the proposed measurement weighting strategy indeed brings improved performance in epitranscriptome module discovery in terms of both module accuracy and biological significance. Although the new approach is integrated with Euclidean distance measurement in a hierarchical clustering scenario, it has great potential to be extended to other distance measurements and algorithms as well for addressing various tasks in epitranscriptome analysis. Additionally, we show for the first time with rigorous statistical analysis that the epitranscriptome modules are biologically meaningful with different GO functions enriched, which established the functional basis of epitranscriptome modules, fulfilled a key prerequisite for functional characterization, and deciphered the epitranscriptome and its regulation.

Epitranscriptomics of cancer

The functional impact of modifications of cellular RNAs, including mRNAs, miRNAs and lncRNAs, is a field of intense study. The role of such modifications in cancer has started to be elucidated. Diverse and sometimes opposite effects of RNA modifications have been reported. Some RNA modifications promote, while others decrease the growth and invasiveness of cancer. The present manuscript reviews the current knowledge on the potential impacts of N6-Methyladenosine, Pseudouridine, Inosine, 2’O-methylation or methylcytidine in cancer’s RNA. It also highlights the remaining questions and provides hints on research avenues and potential therapeutic applications, whereby modulating dynamic RNA modifications may be a new method to treat cancer.

RNA N6-methyladenosine methyltransferase-like 3 promotes liver cancer progression through YTHDF2-dependent posttranscriptional silencing of SOCS2

Epigenetic alterations have contributed greatly to human carcinogenesis. Conventional epigenetic studies have predominantly focused on DNA methylation, histone modifications, and chromatin remodeling. Recently, diverse and reversible chemical modifications of RNAs have emerged as a new layer of epigenetic regulation. N6-methyladenosine (m6A) is the most abundant chemical modification of eukaryotic messenger RNA (mRNA) and is important for the regulation of mRNA stability, splicing, and translation. Using transcriptome sequencing, we discovered that methyltransferase-like 3 (METTL3), a major RNA N6-adenosine methyltransferase, was significantly up-regulated in human hepatocellular carcinoma (HCC) and multiple solid tumors. Clinically, overexpression of METTL3 is associated with poor prognosis of patients with HCC. Functionally, we proved that knockdown of METTL3 drastically reduced HCC cell proliferation, migration, and colony formation in vitro. Knockout of METTL3 remarkably suppressed HCC tumorigenicity and lung metastasis in vivo. On the other hand, using the CRISPR/dCas9-VP64 activation system, we demonstrated that overexpression of METTL3 significantly promoted HCC growth both in vitro and in vivo. Through transcriptome sequencing, m6A sequencing, and m6A methylated RNA immuno-precipitation quantitative reverse-transcription polymerase chain reaction, we identified suppressor of cytokine signaling 2 (SOCS2) as a target of METTL3-mediated m6A modification. Knockdown of METTL3 substantially abolished SOCS2 mRNA m6A modification and augmented SOCS2 mRNA expression. We also showed that m6A-mediated SOCS2 mRNA degradation relied on the m6A reader protein YTHDF2-dependent pathway.

CONCLUSION

METTL3 is frequently up-regulated in human HCC and contributes to HCC progression. METTL3 represses SOCS2 expression in HCC through an m6A-YTHDF2-dependent mechanism. Our findings suggest an important mechanism of epigenetic alteration in liver carcinogenesis. (Hepatology 2018;67:2254-2270).

Adenosine methylation as a molecular imprint defining the fate of RNA

Multiple lines of evidence suggest the RNA modification N⁶‐methyladonsine (m⁶A), which is installed in the nucleus cotranscriptionally and, thereafter, serves as a reversible chemical imprint that influences several steps of mRNA metabolism. This includes but is not limited to RNA folding, splicing, stability, transport and translation. In this Review we focus on the current view of the nuclear installation of m⁶A as well as the molecular players involved, the so called m⁶A writers. We also explore the effector proteins, or m⁶A readers, that decode the imprint in different cellular contexts and compartments, and ultimately, the way the modification influences the lifecycle of an RNA molecule. The wide evolutionary conservation of m⁶A and its critical role in physiology and disease warrants further studies into this burgeoning and exciting field.

The Role of Dynamic m6 A RNA Methylation in Photobiology

N⁶ -methyladenosine (m⁶ A) is the most abundant internal RNA modification among numerous post-transcriptional modifications identified in eukaryotic mRNA. m⁶ A modification of RNA is catalyzed by the "writer" m⁶ A methyltransferase enzyme complex, consisting of METTL3, METTL14, WTAP and KIAA1429. The m⁶ A modification is reversible and can be removed by "eraser" m⁶ A demethylase enzymes, namely, FTO and ALKBH5. The biological function of m⁶ A modification on RNA is carried out by RNA-binding effector proteins called "readers." Varied functions of the reader proteins regulate mRNA metabolism by affecting stability, translation, splicing or nuclear export. The epitranscriptomic gene regulation by m⁶ A RNA methylation regulates various pathways, which contribute to basic cellular processes essential for cell maintenance, development and cell fate, and affect response to external stimuli and stressors. In this review, we summarize the recent advances in the regulation and function of m⁶ A RNA methylation, with a focus on UV-induced DNA damage response and the circadian clock machinery. Insights into the mechanisms of m⁶ A RNA regulation and post-transcriptional regulatory function in these biological processes may facilitate the development of new preventive and therapeutic strategies for various diseases related to dysregulation of UV damage response and circadian rhythm.

Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism

N⁶-methyladenosine (m⁶A) is a chemical modification present in multiple RNA species, being most abundant in mRNAs. Studies on enzymes or factors that catalyze, recognize, and remove m⁶A have revealed its comprehensive roles in almost every aspect of mRNA metabolism, as well as in a variety of physiological processes. This review describes the current understanding of the m⁶A modification, particularly the functions of its writers, erasers, readers in RNA metabolism, with an emphasis on its role in regulating the isoform dosage of mRNAs.

Region-specific RNA m6A methylation represents a new layer of control in the gene regulatory network in the mouse brain

N⁶-methyladenosine (m⁶A) is the most abundant epitranscriptomic mark found on mRNA and has important roles in various physiological processes. Despite the relatively high m⁶A levels in the brain, its potential functions in the brain remain largely unexplored. We performed a transcriptome-wide methylation analysis using the mouse brain to depict its region-specific methylation profile. RNA methylation levels in mouse cerebellum are generally higher than those in the cerebral cortex. Heterogeneity of RNA methylation exists across different brain regions and different types of neural cells including the mRNAs to be methylated, their methylation levels and methylation site selection. Common and region-specific methylation have different preferences for methylation site selection and thereby different impacts on their biological functions. In addition, high methylation levels of fragile X mental retardation protein (FMRP) target mRNAs suggest that m⁶A methylation is likely to be used for selective recognition of target mRNAs by FMRP in the synapse. Overall, we provide a region-specific map of RNA m⁶A methylation and characterize the distinct features of specific and common methylation in mouse cerebellum and cerebral cortex. Our results imply that RNA m⁶A methylation is a newly identified element in the region-specific gene regulatory network in the mouse brain.

N 6 -methyl-adenosine level in Nicotiana tabacum is associated with tobacco mosaic virus

BACKGROUND

N 6 -methyl-adenosine (m6A) is a prevalent RNA modification in many species. Abnormal m6A methylation levels can lead to RNA dysfunction and can cause diseases. Tobacco mosaic virus (TMV) is one of the most devastating viruses for agricultural plants. It has many hosts, particularly including tobacco and other members the family Solanaceae. However, it remains unclear whether the abnormal growth induced by TMV is associated with the m6A level.

METHODS

A rapid and accurate analytical method using ultra-high-performance liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-HR - MS/MS) was developed to analyse the adenosine (A), cytidine (C), guanosine (G), uridine (U), and m6A contents in the tobacco leaf, and the m6A/G ratio was used to evaluate the m6A level. Subsequent protein sequence alignments were used to find the potential methylases and demethylases in Nicotiana tabacum (N. tabacum). Finally, reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) was used to analyse the gene expression levels of the potential methylases and demethylases in the N. tabacum leaf.

RESULTS

The results showed that TMV reduced the m6A level. Moreover, protein sequence alignments revealed partial homology among human ALKBH5, Arabidopsis (NP_001031793), and Nicotiana sylvestris (XP_009800010). The gene expression level of the potential demethylase XM_009801708 increased at 14 and 21 days in N. tabacum infected with TMV, whereas all of the potential methylases decreased.

CONCLUSIONS

The reversible m6A modification in N. tabacum mRNA might represent a novel epigenetic mechanism involved in TMV.

Mechanism of N6-methyladenosine modification and its emerging role in cancer

N⁶-methyladenosine (m⁶A), the most prevalent internal methylation in messenger RNA (mRNA) that is deposited by m⁶A methyltransferases, removed by m⁶A demethylases and recognized by different RNA-binding proteins, distinguishes the transcripts through multilayer interactions with mRNA processing, export, degradation and translation machineries. m⁶A plays an important role in regulation of gene expression for fundamental cellular processes and diverse physiological functions. Aberrant m⁶A decorations lead to cancer but also have the potential to yield new therapies. This review outlines the evolution of the m⁶A field, formation of key concepts, important open questions and also discusses the molecular basis of mRNA m⁶A modification and its effect in cancer, highlighting the potential of demethylase as a therapeutic target for cancer treatment.

RNA N6-methyladenosine modification in cancers: current status and perspectives

N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic messenger RNAs (mRNAs), has been shown to play critical roles in various normal bioprocesses such as tissue development, stem cell self-renewal and differentiation, heat shock or DNA damage response, and maternal-to-zygotic transition. The m6A modification is deposited by the m6A methyltransferase complex (MTC; i.e., writer) composed of METTL3, METTL14 and WTAP, and probably also VIRMA and RBM15, and can be removed by m6A demethylases (i.e., erasers) such as FTO and ALKBH5. The fates of m6A-modified mRNAs rely on the functions of distinct proteins that recognize them (i.e., readers), which may affect the stability, splicing, and/or translation of target mRNAs. Given the functional importance of the m6A modification machinery in normal bioprocesses, it is not surprising that evidence is emerging that dysregulation of m6A modification and the associated proteins also contributes to the initiation, progression, and drug response of cancers. In this review, we focus on recent advances in the study of biological functions and the underlying molecular mechanisms of dysregulated m6A modification and the associated machinery in the pathogenesis and drug response of various types of cancers. In addition, we also discuss possible therapeutic interventions against the dysregulated m6A machinery to treat cancers.

Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development

The N6-methyladenosine (m6A) modification is the most prevalent internal RNA modification in eukaryotes. The majority of m6A sites are found in the last exon and 3' UTRs. Here we show that the nuclear m6A reader YTHDC1 is essential for embryo viability and germline development in mouse. Specifically, YTHDC1 is required for spermatogonial development in males and for oocyte growth and maturation in females; Ythdc1-deficient oocytes are blocked at the primary follicle stage. Strikingly, loss of YTHDC1 leads to extensive alternative polyadenylation in oocytes, altering 3' UTR length. Furthermore, YTHDC1 deficiency causes massive alternative splicing defects in oocytes. The majority of splicing defects in mutant oocytes are rescued by introducing wild-type, but not m6A-binding-deficient, YTHDC1. YTHDC1 is associated with the pre-mRNA 3' end processing factors CPSF6, SRSF3, and SRSF7. Thus, YTHDC1 plays a critical role in processing of pre-mRNA transcripts in the oocyte nucleus and may have similar non-redundant roles throughout fetal development.

The YTH Domain Protein ECT2 Is an m6A Reader Required for Normal Trichome Branching in Arabidopsis

Methylations at position N⁶ of internal adenosines (m⁶As) are the most abundant and widespread mRNA modifications. These modifications play crucial roles in reproduction, growth, and development by controlling gene expression patterns at the posttranscriptional level. Their function is decoded by readers that share the YTH domain, which forms a hydrophobic pocket that directly accommodates the m⁶A residues. While the physiological and molecular functions of YTH readers have been extensively studied in animals, little is known about plant readers, even though m⁶As are crucial for plant survival and development. Viridiplantae contains high numbers of YTH domain proteins. Here, we performed comprehensive evolutionary analysis of YTH domain proteins and demonstrated that they are highly likely to be actual readers with redundant as well as specific functions. We also show that the ECT2 protein from Arabidopsis thaliana binds to m⁶A-containing RNAs in vivo and that this property relies on the m⁶A binding pocket carried by its YTH domain. ECT2 is cytoplasmic and relocates to stress granules upon heat exposure, suggesting that it controls mRNA fate in the cytosol. Finally, we demonstrate that ECT2 acts to decode the m⁶A signal in the trichome and is required for their normal branching through controlling their ploidy levels.

The m6A Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis

The epitranscriptomic mark N⁶-methyladenosine (m⁶A) can be written, read, and erased via the action of a complex network of proteins. m⁶A binding proteins read m⁶A marks and transduce their downstream regulatory effects by altering RNA metabolic processes. The characterization of m⁶A readers is an essential prerequisite for understanding the roles of m⁶A in plants, but the identities of m⁶A readers have been unclear. Here, we characterized the YTH-domain family protein ECT2 as an Arabidopsis thaliana m⁶A reader whose m⁶A binding function is required for normal trichome morphology. We developed the formaldehyde cross-linking and immunoprecipitation method to identify ECT2-RNA interaction sites at the transcriptome-wide level. This analysis demonstrated that ECT2 binding sites are strongly enriched in the 3' untranslated regions (3' UTRs) of target genes and led to the identification of a plant-specific m⁶A motif. Sequencing analysis suggested that ECT2 plays dual roles in regulating 3' UTR processing in the nucleus and facilitating mRNA stability in the cytoplasm. Disruption of ECT2 accelerated the degradation of three ECT2 binding transcripts related to trichome morphogenesis, thereby affecting trichome branching. The results shed light on the underlying mechanisms of the roles of m⁶A in RNA metabolism, as well as plant development and physiology.

YTH Domain: A Family of N6-methyladenosine (m6A) Readers

Like protein and DNA, different types of RNA molecules undergo various modifications. Accumulating evidence suggests that these RNA modifications serve as sophisticated codes to mediate RNA behaviors and many important biological functions. N⁶-methyladenosine (m⁶A) is the most abundant internal RNA modification found in a variety of eukaryotic RNAs, including but not limited to mRNAs, tRNAs, rRNAs, and long non-coding RNAs (lncRNAs). In mammalian cells, m⁶A can be incorporated by a methyltransferase complex and removed by demethylases, which ensures that the m⁶A modification is reversible and dynamic. Moreover, m⁶A is recognized by the YT521-B homology (YTH) domain-containing proteins, which subsequently direct different complexes to regulate RNA signaling pathways, such as RNA metabolism, RNA splicing, RNA folding, and protein translation. Herein, we summarize the recent progresses made in understanding the molecular mechanisms underlying the m⁶A recognition by YTH domain-containing proteins, which would shed new light on m⁶A-specific recognition and provide clues to the future identification of reader proteins of many other RNA modifications.

Structural Insights into N6-methyladenosine (m6A) Modification in the Transcriptome

More than 100 types of chemical modifications in RNA have been well documented. Recently, several modifications, such as N⁶-methyladenosine (m⁶A), have been detected in mRNA, opening the window into the realm of epitranscriptomics. The m⁶A modification is the most abundant modification in mRNA and non-coding RNA (ncRNA). At the molecular level, m⁶A affects almost all aspects of mRNA metabolism, including splicing, translation, and stability, as well as microRNA (miRNA) maturation, playing essential roles in a range of cellular processes. The m⁶A modification is regulated by three classes of proteins generally referred to as the “writer” (adenosine methyltransferase), “eraser” (m⁶A demethylating enzyme), and “reader” (m⁶A-binding protein). The m⁶A modification is reversibly installed and removed by writers and erasers, respectively. Readers, which are members of the YT521-B homology (YTH) family proteins, selectively bind to RNA and affect its fate in an m⁶A-dependent manner. In this review, we summarize the structures of the functional proteins that modulate the m⁶A modification, and provide our insights into the m⁶A-mediated gene regulation.

Epigenetics and epitranscriptomics in temporal patterning of cortical neural progenitor competence

Yoon et al. review epigenetic and epitranscriptomic mechanisms that regulate the lineage specification of neural progenitor cells in the developing brain.

During embryonic brain development, neural progenitor/stem cells (NPCs) sequentially give rise to different subtypes of neurons and glia via a highly orchestrated process. To accomplish the ordered generation of distinct progenies, NPCs go through multistep transitions of their developmental competence. The molecular mechanisms driving precise temporal coordination of these transitions remains enigmatic. Epigenetic regulation, including changes in chromatin structures, DNA methylation, and histone modifications, has been extensively investigated in the context of cortical neurogenesis. Recent studies of chemical modifications on RNA, termed epitranscriptomics, have also revealed their critical roles in neural development. In this review, we discuss advances in understanding molecular regulation of the sequential lineage specification of NPCs in the embryonic mammalian brain with a focus on epigenetic and epitranscriptomic mechanisms. In particular, the discovery of lineage-specific gene transcripts undergoing rapid turnover in NPCs suggests that NPC developmental fate competence is determined much earlier, before the final cell division, and is more tightly controlled than previously appreciated. We discuss how multiple regulatory systems work in harmony to coordinate NPC behavior and summarize recent findings in the context of a model of epigenetic and transcriptional prepatterning to explain NPC developmental competence.

The Emerging Field of Epitranscriptomics in Neurodevelopmental and Neuronal Disorders

Analogous to DNA methylation and histone modifications, RNA modifications represent a novel layer of regulation of gene expression. The dynamic nature and increasing number of RNA modifications offer new possibilities to rapidly alter gene expression upon specific environmental changes. Recent lines of evidence indicate that modified RNA molecules and associated complexes regulating and “reading” RNA modifications play key roles in the nervous system of several organisms, controlling both, its development and function. Mutations in several human genes that modify transfer RNA (tRNA) have been linked to neurological disorders, in particular to intellectual disability. Loss of RNA modifications alters the stability of tRNA, resulting in reduced translation efficiency and generation of tRNA fragments, which can interfere with neuronal functions. Modifications present on messenger RNAs (mRNAs) also play important roles during brain development. They contribute to neuronal growth and regeneration as well as to the local regulation of synaptic functions. Hence, potential combinatorial effects of RNA modifications on different classes of RNA may represent a novel code to dynamically fine tune gene expression during brain function. Here we discuss the recent findings demonstrating the impact of modified RNAs on neuronal processes and disorders.

Emerging role of dynamic RNA modifications during animal development

The central dogma of molecular biology statically says that the information flows from DNA to messenger RNA to protein. But the recent advances in mass spectrometry and high throughput technology have helped the scientists to view RNA as little more than a courier of genetic information encoded in the DNA. The dynamics of RNA modifications in coding and non-coding RNAs are just emerging as a carrier of non-genetic information, uncovering a new layer of complexity in the regulation of gene expression and protein translation. In this review, we summarize about the current knowledge of N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C) and pseudouridine (Ψ) modifications in RNA, and described how these RNA modifications are implicated in early animal development and in several human diseases.

DNA Methylation and Psychiatric Disorders

DNA methylation has been an important area of research in the study of molecular mechanism to psychiatric disorders. Recent evidence has suggested that abnormalities in global methylation, methylation of genes, and pathways could play a role in the etiology of many forms of mental illness. In this article, we review the mechanisms of DNA methylation, including the genetic and environmental factors affecting methylation changes. We report and discuss major findings regarding DNA methylation in psychiatric patients, both within the context of global methylation studies and gene-specific methylation studies. Finally, we discuss issues surrounding data quality improvement, the limitations of current methylation analysis methods, and the possibility of using DNA methylation-based treatment for psychiatric disorders in the future.

Distinct and Modular Organization of Protein Interacting Sites in Long Non-coding RNAs

Background: Long non-coding RNAs (lncRNAs), are being reported to be extensively involved in diverse regulatory roles and have exhibited numerous disease associations. LncRNAs modulate their function through interaction with other biomolecules in the cell including DNA, RNA, and proteins. The availability of genome-scale experimental datasets of RNA binding proteins (RBP) motivated us to understand the role of lncRNAs in terms of its interactions with these proteins. In the current report, we demonstrate a comprehensive study of interactions between RBP and lncRNAs at a transcriptome scale through extensive analysis of the crosslinking and immunoprecipitation (CLIP) experimental datasets available for 70 RNA binding proteins.

Results: Our analysis suggests that density of interaction sites for these proteins was significantly higher for specific sub-classes of lncRNAs when compared to protein-coding transcripts. We also observe a positional preference of these RBPs across lncRNA and protein coding transcripts in addition to a significant co-occurrence of RBPs having similar functions, suggesting a modular organization of these elements across lncRNAs.

Conclusion: The significant enrichment of RBP sites across some lncRNA classes is suggestive that these interactions might be important in understanding the functional role of lncRNA. We observed a significant enrichment of RBPs which are involved in functional roles such as silencing, splicing, mRNA processing, and transport, indicating the potential participation of lncRNAs in such processes.

Interactions, localization, and phosphorylation of the m6A generating METTL3-METTL14-WTAP complex

N⁶-methyladenine (m⁶A) is found on many eukaryotic RNAs including mRNAs. m⁶A modification has been implicated in mRNA stability and turnover, localization, or translation efficiency. A heterodimeric enzyme complex composed of METTL3 and METTL14 generates m⁶A on mRNAs. METTL3/14 is found in the nucleus where it is localized to nuclear speckles and the splicing regulator WTAP is required for this distinct nuclear localization pattern. Although recent crystal structures revealed how the catalytic MT-A70 domains of METTL3 and METTL14 interact with each other, a more global architecture including WTAP and RNA interactions has not been reported so far. Here, we used recombinant proteins and mapped binding surfaces within the METTL3/14-WTAP complex. Furthermore, we identify nuclear localization signals and identify phosphorylation sites on the endogenous proteins. Using an in vitro methylation assay, we confirm that monomeric METTL3 is soluble and inactive while the catalytic center of METTL14 is degenerated and thus also inactive. In addition, we show that the C-terminal RGG repeats of METTL14 are required for METTL3/14 activity by contributing to RNA substrate binding. Our biochemical work identifies characteristic features of METTL3/14-WTAP and reveals novel insight into the overall architecture of this important enzyme complex.

Emerging Roles of N6-Methyladenosine on HIV-1 RNA Metabolism and Viral Replication

N⁶-methyladenosine (m⁶A) is the most abundant internal modification present in Eukaryotic mRNA. The functions of this chemical modification are mediated by m⁶A-binding proteins (m⁶A readers) and regulated by methyltransferases (m⁶A writers) and demethylases (m⁶A erasers), which together are proposed to be responsible of a new layer of post-transcriptional control of gene expression. Despite the presence of m⁶A in a retroviral genome was reported more than 40 years ago, the recent development of sequencing-based technologies allowing the mapping of m⁶A in a transcriptome-wide manner made it possible to identify the topology and dynamics of m⁶A during replication of HIV-1 as well as other viruses. As such, three independent groups recently reported the presence of m⁶A along the HIV-1 genomic RNA (gRNA) and described the impact of cellular m⁶A writers, erasers and readers on different steps of viral RNA metabolism and replication. Interestingly, while two groups reported a positive role of m⁶A at different steps of viral gene expression it was also proposed that the presence of m⁶A within the gRNA reduces viral infectivity by inducing the early degradation of the incoming viral genome. This review summarizes the recent advances in this emerging field and discusses the relevance of m⁶A during HIV-1 replication.

Solution structure of the RNA recognition domain of METTL3-METTL14 N6-methyladenosine methyltransferase

N⁶-methyladenosine (m⁶A), a ubiquitous RNA modification, is installed by METTL3-METTL14 complex. The structure of the heterodimeric complex between the methyltransferase domains (MTDs) of METTL3 and METTL14 has been previously determined. However, the MTDs alone possess no enzymatic activity. Here we present the solution structure for the zinc finger domain (ZFD) of METTL3, the inclusion of which fulfills the methyltransferase activity of METTL3-METTL14. We show that the ZFD specifically binds to an RNA containing 5′-GGACU-3′ consensus sequence, but does not to one without. The ZFD thus serves as the target recognition domain, a structural feature previously shown for DNA methyltransferases, and cooperates with the MTDs of METTL3-METTL14 for catalysis. However, the interaction between the ZFD and the specific RNA is extremely weak, with the binding affinity at several hundred micromolar under physiological conditions. The ZFD contains two CCCH-type zinc fingers connected by an anti-parallel β-sheet. Mutational analysis and NMR titrations have mapped the functional interface to a contiguous surface. As a division of labor, the RNA-binding interface comprises basic residues from zinc finger 1 and hydrophobic residues from β-sheet and zinc finger 2. Further we show that the linker between the ZFD and MTD of METTL3 is flexible but partially folded, which may permit the cooperation between the two domains during catalysis. Together, the structural characterization of METTL3 ZFD paves the way to elucidate the atomic details of the entire process of RNA m⁶A modification.

FTO reduces mitochondria and promotes hepatic fat accumulation through RNA demethylation

Fat mass and obesity-associated protein (FTO) is a RNA demethylase, whether FTO regulates fat metabolism through its demethylation is unclear. The results of this study confirmed that N6-methyladenosine (m⁶ A) is associated with fat accumulation both in vivo and in vitro. The data showed that FTO down-regulated m⁶ A levels, decreased mitochondrial content, and increased triglyceride (TG) deposition. However, an FTO (R316A) mutant lacking demethylation activity could not regulate mitochondria and TG content, indicating that FTO affects mitochondrial content and fat metabolism by modulating m⁶ A levels in hepatocytes. In addition, the regulatory roles of cycloleucine (methylation inhibitor) and betaine (methyl donor) could regulate m⁶ A levels and fat deposition. This work clarified that the demethylation function of FTO plays an essential role in the fat metabolism of hepatocytes and links the epigenetic modification of RNA with fat deposition, thereby providing a new target (m⁶ A) for regulation of hepatic fat metabolism.

Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d

In this study, Knuckles et al. identified Flacc/Zc3h13 as a novel interactor of m⁶A methyltransferase complex components in Drosophila and mice. They show that Flacc promotes the recruitment of the methyltransferase to mRNA by bridging Fl(2)d to the mRNA-binding factor Nito, providing novel insights into the conservation and regulation of the m⁶A machinery.

N⁶-methyladenosine (m⁶A) is the most abundant mRNA modification in eukaryotes, playing crucial roles in multiple biological processes. m⁶A is catalyzed by the activity of methyltransferase-like 3 (Mettl3), which depends on additional proteins whose precise functions remain poorly understood. Here we identified Zc3h13 (zinc finger CCCH domain-containing protein 13)/Flacc [Fl(2)d-associated complex component] as a novel interactor of m⁶A methyltransferase complex components in Drosophila and mice. Like other components of this complex, Flacc controls m⁶A levels and is involved in sex determination in Drosophila. We demonstrate that Flacc promotes m⁶A deposition by bridging Fl(2)d to the mRNA-binding factor Nito. Altogether, our work advances the molecular understanding of conservation and regulation of the m⁶A machinery.

Precise Antibody-Independent m6A Identification via 4SedTTP-Involved and FTO-Assisted Strategy at Single-Nucleotide Resolution

Innovative detection techniques to achieve precise m6A distribution within mammalian transcriptome can advance our understanding of its biological functions. We specifically introduced the atom-specific replacement of oxygen with progressively larger atoms (sulfur and selenium) at 4-position of deoxythymidine triphosphate to weaken its ability to base pair with m6A, while maintaining A-T* base pair virtually the same as the natural one. 4SedTTP turned out to be an outstanding candidate that endowed m6A with a specific signature of RT truncation, thereby making this "RT-silent" modification detectable with the assistance of m6A demethylase FTO through next-generation sequencing. This antibody-independent, 4SedTTP-involved and FTO-assisted strategy is applicable in m6A identification, even for two closely gathered m6A sites, within an unknown region at single-nucleotide resolution.

METTL3 regulates alternative splicing of MyD88 upon the lipopolysaccharide-induced inflammatory response in human dental pulp cells

Dental pulp inflammation is a widespread public health problem caused by oral bacterial infections and can progress to pulp necrosis and periapical diseases. N6‐methyladenosine (m6A) is a prevalent epitranscriptomic modification in mRNA. Previous studies have demonstrated that m6A methylation plays important roles in cell differentiation, embryonic development and stress responses. However, whether m6A modification affects dental pulp inflammation remains unknown. To address this issue, we investigated the expression of m6A and N6‐adenosine methyltransferase (METTL3, METTL14) as well as demethylases (FTO, ALKBH5) and found that the levels of m6A and METTL3 were up‐regulated in human dental pulp cells (HDPCs) stimulated by lipopolysaccharide (LPS). Furthermore, we knocked down METTL3 and demonstrated that METTL3 depletion decreased the expression of inflammatory cytokines and the phosphorylation of IKKα/β, p65 and IκBα in the NF‐κB signalling pathway as well as p38, ERK and JNK in the MAPK signalling pathway in LPS‐induced HDPCs. The RNA sequencing analysis revealed that the vast number of genes affected by METTL3 depletion was associated with the inflammatory response. Previous research has shown that METTL3‐dependent N6‐adenosine methylation plays an important role in mRNA splicing. In this study, we found that METTL3 knockdown facilitated the expression of MyD88S, a splice variant of MyD88 that inhibits inflammatory cytokine production, suggesting that METTL3 might inhibit the LPS‐induced inflammatory response of HDPCs by regulating alternative splicing of MyD88. These data shed light on new findings in epitranscriptomic regulation of the inflammatory response and open new avenues for research into the molecular mechanisms of dental pulp inflammation.

Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d

N⁶-methyladenosine (m⁶A) is the most abundant mRNA modification in eukaryotes, playing crucial roles in multiple biological processes. m⁶A is catalyzed by the activity of methyltransferase-like 3 (Mettl3), which depends on additional proteins whose precise functions remain poorly understood. Here we identified Zc3h13 (zinc finger CCCH domain-containing protein 13)/Flacc [Fl(2)d-associated complex component] as a novel interactor of m⁶A methyltransferase complex components in Drosophila and mice. Like other components of this complex, Flacc controls m⁶A levels and is involved in sex determination in Drosophila We demonstrate that Flacc promotes m⁶A deposition by bridging Fl(2)d to the mRNA-binding factor Nito. Altogether, our work advances the molecular understanding of conservation and regulation of the m⁶A machinery.

Wilms' tumor 1-associating protein promotes renal cell carcinoma proliferation by regulating CDK2 mRNA stability

Background

Wilms’ tumor 1-associating protein (WTAP) plays an important role in physiological processes and the development of tumor such as cell cycle regulation. The regulation of cell cycle is mainly dependent on cyclins and cyclin-dependent protein kinases (CDKs). Recent studies have shown that CDKs are closely related to the tumor diagnosis, progression and response to treatment. However, their specific biological roles and related mechanism in renal cell carcinoma (RCC) remain unknown.

Methods

Quantitative real-time PCR, western blotting and immunohistochemistry were used to detect the expression of WTAP and CDK2. The survival analysis was adopted to explore the association between WTAP expression and the prognosis of RCC. Cells were stably transfected with lentivirus approach and cell proliferation and cell cycle, as well as tumorigenesis in nude mice were performed to assess the effect of WTAP in RCC. RNA immunoprecipitation, Luciferase reporter assay and siRNA were employed to identify the direct binding sites of WTAP with CDK2 transcript. Colony formation assay was conducted to confirm the function of CDK2 in WTAP-induced growth promoting.

Results

In RCC cell lines and tissues, WTAP was significantly over-expressed. Compared with patients with low expression of WTAP, patients with high expression of WTAP had lower overall survival rate. Additionally, cell function test indicated that cell proliferation abilities in WTAP over-expressed group were enhanced, while WTAP knockdown showed the opposite results. Subcutaneous xenograft tumor model displayed that knockdown of WTAP could impede tumorigenesis in vivo. Mechanism study exhibited that CDK2 expression was positively associated with the expression of WTAP. Moreover, WTAP stabilized CDK2 transcript to enhance CDK2 expression via binding to 3′-UTR of CDK2 transcript. Additionally, specific inhibitors of CDK2 activity and small interfering RNA (siRNA) of CDK2 expression inhibited WTAP-mediated promotion of proliferation.

Conclusions

These findings suggest that WTAP may have an oncogenic role in RCC through physically binding to CDK2 transcript and enhancing its transcript stability which might provide new insights into RCC therapy.

Electronic supplementary material

The online version of this article (10.1186/s13046-018-0706-6) contains supplementary material, which is available to authorized users.

VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation

N⁶-methyladenosine (m⁶A) is enriched in 3'untranslated region (3'UTR) and near stop codon of mature polyadenylated mRNAs in mammalian systems and has regulatory roles in eukaryotic mRNA transcriptome switch. Significantly, the mechanism for this modification preference remains unknown, however. Herein we report a characterization of the full m⁶A methyltransferase complex in HeLa cells identifying METTL3/METTL14/WTAP/VIRMA/HAKAI/ZC3H13 as the key components, and we show that VIRMA mediates preferential mRNA methylation in 3'UTR and near stop codon. Biochemical studies reveal that VIRMA recruits the catalytic core components METTL3/METTL14/WTAP to guide region-selective methylations. Around 60% of VIRMA mRNA immunoprecipitation targets manifest strong m⁶A enrichment in 3'UTR. Depletions of VIRMA and METTL3 induce 3'UTR lengthening of several hundred mRNAs with over 50% targets in common. VIRMA associates with polyadenylation cleavage factors CPSF5 and CPSF6 in an RNA-dependent manner. Depletion of CPSF5 leads to significant shortening of 3'UTR of over 2800 mRNAs, 84% of which are modified with m⁶A and have increased m⁶A peak density in 3'UTR and near stop codon after CPSF5 knockdown. Together, our studies provide insights into m⁶A deposition specificity in 3'UTR and its correlation with alternative polyadenylation.

Deciphering the Epitranscriptome in Cancer

Technological and methodological advancements have recently revolutionized our understanding of widespread epitranscriptome including RNA modifications and editing. N⁶-methyladenosine (m⁶A) represents the most prevalent internal modification in mammalian RNAs. Adenosine to inosine (A-to-I) RNA editing is an important mechanism underlying RNA generation and protein diversity through the post-transcriptional modification of single nucleotides in RNA sequences. In this review, we attempt to summarize its functional importance in various fundamental bioprocesses of m⁶A and A-to-I editing. We also highlight some of the key findings that have helped shape our understanding of epitranscriptome in tumorigenesis, tumor progression, and metastasis. Finally, we discuss conceivable targets and future directions of m⁶A and A-to-I editing in cancer therapeutics.