Emerging role of RNA modification N6-methyladenosine in immune evasion

The innate and adaptive immune cells have complex signaling pathways for sensing and initiating immune responses against disease. These pathways are interrupted at different levels to occur immune evasion, including by N6-methyladenosine (m6A) modification. In this review, we discuss studies revealing the immune evasion mechanism by m6A modification, which underlies the retouching of these signaling networks and the rapid tolerance of innate and adaptive immune molecules during disease. We also focus on the functions of m6A in main chemokines regulation, and their roles in promotive and suppressive immune cell recruitment. We then discuss some of the current challenges in the field and describe future directions for the immunological mechanisms of m6A modification.Subject terms: Immunosurveillance, RNA modification     

The RNA N6-methyladenosine demethylase ALKBH9B modulates ABA responses in Arabidopsis

The mRNA modification N⁶-methyladenosine(m⁶A)plays vital roles in plant development and biotic and abiotic stress responses.The RNA m⁶A demethylase ALKBH9 B can remove m⁶A in alfalfa mosaic virus RNA and plays roles in alfalfa mosaic virus infection in Arabidopsis.However,it is unknown whether ALKBH9 B also exhibits demethylation activity and has a biological role in endogenous plant mRNA.We demonstrated here that mRNA m⁶A modification is in...     

A dynamic reversible RNA N6-methyladenosine modification: current status and perspectives

N⁶-methyladenosine (m⁶A), as the most abundant RNA epigenetic modifications, has been shown to play critical roles in various biological functions. Research about enzymes that can catalyze and remove m⁶A have revealed its comprehensive roles in messenger RNA (mRNA) metabolism and other physiological processes. The “readers” including YTH domain-containing proteins, hnRNPC, hnRNPG, hnRNPA2B1, IGF2BP1, IGF2BP2, and IGF2BP3, which can affect the fates of mRNA in an m⁶A-dependent manner. In this review, we focus on recent advances in the research of the m⁶A modifications, especially about the latest functions of its writers, erasers, readers in RNA metabolism, cancer, and lipid metabolism. In the end, we provide insights into the underlying molecular mechanisms of m⁶A modifications.     

Regulation of RNA N6-methyladenosine modification and its emerging roles in skeletal muscle development

N⁶-methyladenosine (m⁶A) is one of the most widespread and highly conserved chemical modifications in cellular RNAs of eukaryotic genomes. Owing to the development of high-throughput m⁶A sequencing, the functions and mechanisms of m⁶A modification in development and diseases have been revealed. Recent studies have shown that RNA m⁶A methylation plays a critical role in skeletal muscle development, which regulates myoblast proliferation and differentiation, and muscle regeneration. Exploration of the functions of m⁶A modification and its regulators provides a deeper understanding of the regulatory mechanisms underlying skeletal muscle development. In the present review, we aim to summarize recent breakthroughs concerning the global landscape of m⁶A modification in mammals and examine the biological functions and mechanisms of enzymes regulating m⁶A RNA methylation. We describe the interplay between m⁶A and other epigenetic modifications and highlight the regulatory roles of m⁶A in development, especially that of skeletal muscle. m⁶A and its regulators are expected to be targets for the treatment of human muscle-related diseases and novel epigenetic markers for animal breeding in meat production.     

Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA

N⁶-methyladenosine (m⁶A) is the most abundant modification in mammalian mRNA and long noncoding RNA (lncRNA). Recent discoveries of two m⁶A demethylases and cell-type and cell-state-dependent m⁶A patterns indicate that m⁶A modifications are highly dynamic and likely play important biological roles for RNA akin to DNA methylation or histone modification. Proposed functions for m⁶A modification include mRNA splicing, export, stability, and immune tolerance; but m⁶A studies have been hindered by the lack of methods for its identification at single nucleotide resolution. Here, we develop a method that accurately determines m⁶A status at any site in mRNA/lncRNA, termed site-specific cleavage and radioactive-labeling followed by ligation-assisted extraction and thin-layer chromatography (SCARLET). The method determines the precise location of the m⁶A residue and its modification fraction, which are crucial parameters in probing the cellular dynamics of m⁶A modification. We applied the method to determine the m⁶A status at several sites in two human lncRNAs and three human mRNAs and found that m⁶A fraction varies between 6% and 80% among these sites. We also found that many m⁶A candidate sites in these RNAs are however not modified. The precise determination of m⁶A status in a long noncoding RNA also enables the identification of an m⁶A-containing RNA structural motif.     

RNA N6-methyladenosine modification promotes auxin biosynthesis required for male meiosis in rice

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N6-methyladenosine demethylase FTO promotes M1 and M2 macrophage activation

Macrophage polarization is the driving force of various inflammatory diseases, especially those involved in M1/M2 imbalance. N6-methyladenosine (m⁶A) is the most prevalent internal mRNA modification in eukaryotes that affects multiple biological processes, including those involved developmental arrest and immune response. However, the role of m⁶A in macrophage polarization remains unclear. This study found that FTO silencing significantly suppressed both M1 and M2 polarization. FTO depletion decreased the phosphorylation levels of IKKα/β, IκBα and p65 in the NF-κB signaling pathway. The expression of STAT1 was downregulated in M1-polarized macrophages while the expression of STAT6 and PPAR-γ decreased in M2 polarization after FTO knockdown. The actinomycin D experiments showed that FTO knockdown accelerated mRNA decay of STAT1 and PPAR-γ. Furthermore, the stability and expression of STAT1 and PPAR-γ mRNAs increased when the m⁶A reader YTHDF2 was silenced. In conclusion, our results suggest that FTO knockdown inhibits the NF-κB signaling pathway and reduces the mRNA stability of STAT1 and PPAR-γ via YTHDF2 involvement, thereby impeding macrophage activation. These findings indicated a previously unrecognized link between FTO and macrophage polarization and might open new avenues for research into the molecular mechanisms of macrophage polarization-related diseases.     

RNA中6-甲基腺嘌呤的研究进展

RNA酶促共价修饰研究, 尤其是m⁶A(6-甲基腺嘌呤), 是RNA生物学研究的一个新兴领域。m⁶A是真核生物mRNA内部序列中最常见的一种转录后修饰形式, 由包含3个独立组分的复合物mRNA: m⁶A甲基转移酶催化生成。最新研究发现肥胖相关蛋白FTO可以脱掉m⁶A上的甲基, 表明该甲基化过程是可逆的。抑制或敲除m⁶A甲基转移酶会引起重要的表型变化, 但是由于过去的检测方法受限, m⁶A确切的作用机制目前为止还不甚清楚。二代测序技术结合免疫沉淀方法为大规模检测m⁶A修饰并研究其作用机制提供了可能。文章主要综述了m⁶A的发现史、生成机制、组织和基因组分布、检测方法、生物学功能等及其最新研究进展, 并通过比较3种IP-seq技术和数据分析的异同及优缺点, 对m⁶A这种RNA表观修饰研究中尚未解决的问题进行了讨论。     

N6-methyladenosine RNA modification in PD-1/PD-L1: Novel implications for immunotherapy

Cancer immunotherapy has been shown to achieve significant antitumor effects in a variety of malignancies. Out of all the immune checkpoint molecules, PD-1/PD-L1 inhibitor therapy has achieved great success. However, only some cancer patients benefit from this treatment strategy owing to drug resistance. Therefore, identifying the underlying modulators of the PD-1/PD-L1 pathway to completely comprehend the mechanisms of anti-PD-1/PD-L1 treatment is crucially important. Recent research has validated that m6A modification plays a critical role in the PD-1/PD-L1 axis, thus regulating the immune response and immunotherapy strategies. In this review, we summarized the latest research on the regulation of m6A modification in PD-1/PD-L1 pathways in cancer proliferation, invasion, and prognosis based on different kinds of cancers and discussed the possible mechanisms. We also reviewed m6A-associated lncRNAs in the regulation of the PD-1/PD-L1 pathway. More importantly, we outlined the influence of m6A modulation on anti-PD-1 therapy and m6A-related molecules that could predict the curative effect of anti-PD-1/PD-L1 therapy. Further studies exploring the definitive regulation of m6A on the PD1/PD-1 pathway and immunotherapy are needed, which may address some of the current limitations in immunotherapy.     

Identification and characterization of N6-methyladenosine modification of circRNAs in glioblastoma

This research systematically profiled the global N6-methyladenosine modification pattern of circular RNAs (circRNAs) in glioblastoma (GBM). Based on RNA methylation sequencing (MeRIP sequencing or N6-methyladenosine sequencing) and RNA sequencing, we described the N6-methyladenosine modification status and gene expression of circRNAs in GBM and normal brain tissues. N6-methyladenosine–related circRNAs were immunoprecipitated and validated by real-time quantitative PCR. Bioinformatics analysis and related screening were carried out. Compared with those of the NC group, the circRNAs from GBM exhibited 1370 new N6-methyladenosine peaks and 1322 missing N6-methyladenosine peaks. Among the loci associated with altered N6-methyladenosine peaks, 1298 were up-regulated and 1905 were down-regulated. The N6-methyladenosine level tended to be positively correlated with circRNA expression. Bioinformatics analysis was used to predict the biological function of N6-methyladenosine–modified circRNAs and the corresponding signalling pathways. In addition, through PCR validation combined with clinical data mining, we identified five molecules of interest (BUB1, C1S, DTHD1, F13A1 and NDC80) that could be initial candidates for further study of the function and mechanism of N6-methyladenosine–mediated GBM development. In conclusion, our findings demonstrated the N6-methyladenosine modification pattern of circRNAs in human GBM, revealing the possible roles of N6-methyladenosine–mediated novel noncoding RNAs in the origin and progression of GBM.     

Viral RNA N6-methyladenosine modification modulates both innate and adaptive immune responses of human respiratory syncytial virus

Human respiratory syncytial virus (RSV) is the leading cause of respiratory tract infections in humans. A well-known challenge in the development of a live attenuated RSV vaccine is that interferon (IFN)-mediated antiviral responses are strongly suppressed by RSV nonstructural proteins which, in turn, dampens the subsequent adaptive immune responses. Here, we discovered a novel strategy to enhance innate and adaptive immunity to RSV infection. Specifically, we found that recombinant RSVs deficient in viral RNA N⁶-methyladenosine (m⁶A) and RSV grown in m⁶A methyltransferase (METTL3)-knockdown cells induce higher expression of RIG-I, bind more efficiently to RIG-I, and enhance RIG-I ubiquitination and IRF3 phosphorylation compared to wild-type virion RNA, leading to enhanced type I IFN production. Importantly, these m⁶A-deficient RSV mutants also induce a stronger IFN response in vivo, are significantly attenuated, induce higher neutralizing antibody and T cell immune responses in mice and provide complete protection against RSV challenge in cotton rats. Collectively, our results demonstrate that inhibition of RSV RNA m⁶A methylation enhances innate immune responses which in turn promote adaptive immunity.     

N6-methyladenosine demethylase FTO promotes growth and metastasis of gastric cancer via m6A modification of caveolin-1 and metabolic regulation of mitochondrial dynamics

Gastric cancer (GC) is the fifth most common tumor and the third most deadly cancer worldwide. N6-methyladenosine (m⁶A) modification has been reported to play a regulatory role in human cancers. However, the exact role of m⁶A in GC remains largely unknown, and the dysregulation of m⁶A on mitochondrial metabolism has never been studied. In the present study, we demonstrated that FTO, a key demethylase for RNA m⁶A modification, was up-regulated in GC tissues, especially in tissues with liver metastasis. Functionally, FTO acted as a promoter for the proliferation and metastasis in GC. Moreover, FTO enhanced the degradation of caveolin-1 mRNA via its demethylation, which regulated the mitochondrial fission/fusion and metabolism. Collectively, our current findings provided some valuable insights into FTO-mediated m⁶A demethylation modification and could be used as a new strategy for more careful surveillance and aggressive therapeutic intervention.Subject terms: Cancer genomics, Gastrointestinal diseases     

N6-methyladenosine demethylase ALKBH5:a novel regulator of proliferation and differentiation of chicken preadipocytes

Previous studies have reported that the N6-methyladenosine demethylase ALKBH5 can regulate adipogenesis in humans.However,its function in birds remains unclear....