N6-methyladenosine(m6A)is an important RNA methylation modification involved in regulating diverse biological processes across multiple species.Hence,the identification of m6A modification sites provides valuable insi...N6-methyladenosine(m6A)is an important RNA methylation modification involved in regulating diverse biological processes across multiple species.Hence,the identification of m6A modification sites provides valuable insight into the biological mechanisms of complex diseases at the post-transcriptional level.Although a variety of identification algorithms have been proposed recently,most of them capture the features of m6A modification sites by focusing on the sequential dependencies of nucleotides at different positions in RNA sequences,while ignoring the structural dependencies of nucleotides in their threedimensional structures.To overcome this issue,we propose a cross-species end-to-end deep learning model,namely CR-NSSD,which conduct a cross-domain representation learning process integrating nucleotide structural and sequential dependencies for RNA m6A site identification.Specifically,CR-NSSD first obtains the pre-coded representations of RNA sequences by incorporating the position information into single-nucleotide states with chaos game representation theory.It then constructs a crossdomain reconstruction encoder to learn the sequential and structural dependencies between nucleotides.By minimizing the reconstruction and binary cross-entropy losses,CR-NSSD is trained to complete the task of m6A site identification.Extensive experiments have demonstrated the promising performance of CR-NSSD by comparing it with several state-of-the-art m6A identification algorithms.Moreover,the results of cross-species prediction indicate that the integration of sequential and structural dependencies allows CR-NSSD to capture general features of m6A modification sites among different species,thus improving the accuracy of cross-species identification.展开更多
Background:Stemness and chemoresistance contribute to cervical cancer recurrence and metastasis.In the current study,we determined the relevant players and role of N^(6)-methyladenine(m^(6)A)RNA methylation in cervica...Background:Stemness and chemoresistance contribute to cervical cancer recurrence and metastasis.In the current study,we determined the relevant players and role of N^(6)-methyladenine(m^(6)A)RNA methylation in cervical cancer progression.Methods:The roles of m^(6)A RNA methylation and centromere protein K(CENPK)in cervical cancer were analyzed using bioinformatics analysis.Methylated RNA immunoprecipitation was adopted to detect m^(6)A modification of CENPK mRNA.Human cervical cancer clinical samples,cell lines,and xenografts were used for analyzing gene expression and function.Immunofluorescence staining and the tumorsphere formation,clonogenic,MTT,and EdU assays were performed to determine cell stemness,chemoresistance,migration,invasion,and proliferation in HeLa and SiHa cells,respectively.Western blot analysis,co-immunoprecipitation,chromatin immunoprecipitation,and luciferase reporter,cycloheximide chase,and cell fractionation assays were performed to elucidate the underlying mechanism.Results:Bioinformatics analysis of public cancer datasets revealed firm links between m^(6)A modification patterns and cervical cancer prognosis,especially through ZC3H13-mediated m^(6)A modification of CENPK mRNA.CENPK expression was elevated in cervical cancer,associated with cancer recurrence,and independently predicts poor patient prognosis[hazard ratio=1.413,95%confidence interval=1.078−1.853,P=0.012].Silencing of CENPK prolonged the overall survival time of cervical cancer-bearing mice and improved the response of cervical cancer tumors to chemotherapy in vivo(P<0.001).We also showed that CENPK was directly bound to SOX6 and disrupted the interactions of CENPK withβ-catenin,which promotedβ-catenin expression and nuclear translocation,facilitated p53 ubiquitination,and led to activation of Wnt/β-catenin signaling,but suppression of the p53 pathway.This dysregulation ultimately enhanced the tumorigenic pathways required for cell stemness,DNA damage repair pathways necessary for cisplatin/carboplatin resistance,epithelial-mesenchymal transition involved in metastasis,and DNA replication that drove tumor cell proliferation.Conclusions:CENPK was shown to have an oncogenic role in cervical cancer and can thus serve as a prognostic indicator and novel target for cervical cancer treatment.展开更多
Growing evidence supports that cancer progression is closely associated with the tumor microenvironment and immune evasion.Importantly,recent studies have revealed the crucial roles of epigenetic regulators in shaping...Growing evidence supports that cancer progression is closely associated with the tumor microenvironment and immune evasion.Importantly,recent studies have revealed the crucial roles of epigenetic regulators in shaping the tumor microenvironment and restoring immune recognition.N^(6)-methyladenosine(m^(6)A)modification,the most prevalent epigenetic modification of mammalian mRNAs,has essential functions in regulating the processing and metabolism of its targeted RNAs,and therefore affects various biological processes including tumorigenesis and progression.Recent studies have demonstrated the critical functions and molecular mechanisms underlying abnormal m^(6)A modification in the regulation of tumor immunity.In this review,we summarize recent research progress in the potential roles of m^(6)A modification in tumor immunoregulation,with a special focus on the anti-tumor processes of immune cells and involvement in immune-associated molecules and pathways.Furthermore,we review current knowledge regarding the close correlation between m6A-related risk signatures and the tumor immune microenvironment landscape,and we discuss the prognostic value and therapeutic efficacy of m^(6)A regulators in a variety of cancer types.展开更多
N6-methyladenosine(m6A)modification is a reversible process promoted by“writers”,inhibited by“erasers”,and processed by“readers”.During the last decade,increasing emphasis has been placed on the underlying roles...N6-methyladenosine(m6A)modification is a reversible process promoted by“writers”,inhibited by“erasers”,and processed by“readers”.During the last decade,increasing emphasis has been placed on the underlying roles of m6A modification owing to their great importance in biological significance.The abnormal regulation of m6A modification will lead to aberrant cellular behavior and various diseases.Recently,studies have demonstrated that m6A modification is closely associated with the genesis and progression of ocular surface diseases(OSDs).This review focus on the role of m6A modification and research progress in OSDs including fungal keratitis,herpes simplex keratitis,immunerelated keratoconjunctival diseases,pterygium,ocular chemical burns,and Graves’ophthalmopathy,which may provide new insights into and prospective applications for OSDs.展开更多
N6-methyladenosine(m^(6)A)RNA modification is a conserved mechanism that regulates the fate of RNA across eukaryotic organisms.Despite its significance,a comprehensive analysis of m^(6)A-related genes in non-model pla...N6-methyladenosine(m^(6)A)RNA modification is a conserved mechanism that regulates the fate of RNA across eukaryotic organisms.Despite its significance,a comprehensive analysis of m^(6)A-related genes in non-model plants,such as kiwifruit,is lacking.Here,we identified 36 m^(6)A-related genes in the kiwifruit genome according to homology and phylogenetic inference.We performed bioinformatics and evolutionary analyses of the writer,eraser,and reader families of m^(6)A modification.Reanalysis of public RNA-seq data collected from samples under various biotic and abiotic stresses indicated that most m^(6)A-related genes were remarkably expressed under different conditions.Through construction of gene co-expression networks,we found significant correlations between several m^(6)A-related genes and transcription factors(TFs)as well as receptor-like genes during the development and ripening of kiwifruit.Furthermore,we performed ATAC-seq assays on diverse kiwifruit tissues to investigate the regulatory mechanisms of m^(6)A-related genes.We identified 10 common open chromatin regions that were present in at least two tissues,and these regions might serve as potential binding sites for MADS protein,C2H2 protein,and other predicted TFs.Our study offers comprehensive insights into the gene family of m^(6)A-related components in kiwifruit,which will lay foundation for exploring mechanisms of post-transcriptional regulation involved in development and adaptation of kiwifruit.展开更多
N^6-methyladenosine(m^6 A) is an essential RNA modification that regulates key cellular processes, including stem cell renewal,cellular differentiation, and response to DNA damage. Unsurprisingly, aberrant m^6 A methy...N^6-methyladenosine(m^6 A) is an essential RNA modification that regulates key cellular processes, including stem cell renewal,cellular differentiation, and response to DNA damage. Unsurprisingly, aberrant m^6 A methylation has been implicated in the development and maintenance of diverse human cancers. Altered m^6 A levels affect RNA processing, mRNA degradation, and translation of mRNAs into proteins, thereby disrupting gene expression regulation and promoting tumorigenesis. Recent studies have reported that the abnormal expression of m^6 A regulatory enzymes affects m^6 A abundance and consequently dysregulates the expression of tumor suppressor genes and oncogenes, including MYC, SOCS2, ADAM19, and PTEN. In this review, we discuss the specific roles of m^6 A missing space "writers", "erasers", and "readers" in normal physiology and how their altered expression promotes tumorigenesis. We also describe the potential of exploiting the aberrant expression of these enzymes for cancer diagnosis, prognosis, and the development of novel therapies.展开更多
Objective:Investigation of the regulatory mechanisms of cell stemness in cholangiocarcinoma(CCA)is essential for developing effective therapies to improve patient outcomes.The purpose of this study was to investigate ...Objective:Investigation of the regulatory mechanisms of cell stemness in cholangiocarcinoma(CCA)is essential for developing effective therapies to improve patient outcomes.The purpose of this study was to investigate the function and regulatory mechanism of m6A modifications in CCA cell stemness.Methods:Interleukin 6(IL-6)treatment was used to induce an inflammatory response,and loss-of-function studies were conducted using mammosphere culture assays.Chromatin immunoprecipitation,polysome profiling,and methylated RNA immunoprecipitation analyses were used to identify signaling pathways.The in vitro findings were verified in a mice model.Results:We first identified that m6A writers were highly expressed in CCAs and further showed that STAT3 directly bound to the gene loci of m6A writers,showing that IL-6/STAT3 signaling regulated expressions of m6A writers.Downregulating m6A writers prevented cell proliferation and migration in vitro and suppressed CCA tumorigenesis in vivo.Notably,the knockdown of m6A writers inhibited CCA cell stemness that was triggered by IL-6 treatment.Mechanistically,IGF2BP2 was bound to CTNNB1 transcripts,significantly enhancing their stability and translation,and conferring stem-like properties.Finally,we confirmed that the combination of m6A writers,IGF2BP2,and CTNNB1 distinguished CCA tissues from normal tissues.Conclusions:Overall,this study showed that the IL-6-triggered inflammatory response facilitated the expressions of m6A writers and cell stemness in an m6A-IGF2BP2-dependent manner.Furthermore,the study showed that m6A modification was a targetable mediator of the response to inflammation factor exposure,was a potential diagnostic biomarker for CCA,and was critical to the progression of CCA.展开更多
Background and Objective N6-methyladenosine(m6A)plays critical roles in many fundamental biological processes and a variety of diseases.The aim of this study was to investigate the effect of the m6ASNPs on lipid level...Background and Objective N6-methyladenosine(m6A)plays critical roles in many fundamental biological processes and a variety of diseases.The aim of this study was to investigate the effect of the m6ASNPs on lipid levels.Methods We examined the association of m6A-SNPs with lipid levels in a GWAS of 188,578 individuals.Furthermore,we performed eQTL and differential expression analyses to add additional information for the identified m6A-SNPs.展开更多
N^(6)-甲基腺嘌呤(N6-methyladenine,m^(6)A)修饰作为信使RNA中广泛存在的一种甲基化修饰,它的动态变化在生命活动和疾病的发生发展中发挥着重要的作用。近年来研究发现,通过改变靶基因的m6A修饰水平可以调控肿瘤的进展,因此,通过小分...N^(6)-甲基腺嘌呤(N6-methyladenine,m^(6)A)修饰作为信使RNA中广泛存在的一种甲基化修饰,它的动态变化在生命活动和疾病的发生发展中发挥着重要的作用。近年来研究发现,通过改变靶基因的m6A修饰水平可以调控肿瘤的进展,因此,通过小分子靶向干预m^(6)A去甲基化酶可作为抗肿瘤的新策略。本文重点讨论了m^(6)A去甲基化酶,包括脂肪含量与肥胖相关蛋白(fat mass and obesity-associated protein,FTO)和AlkB同源蛋白5(AlkB homlog5,ALKBH5)的作用方式以及它们在肿瘤中发挥的生物学功能,并总结了m^(6)A去甲基化酶小分子抑制剂的研究进展。展开更多
Amyotrophic lateral sclerosis(ALS)is a progressive neurogenerative disorder with uncertain origins.Emerging evidence implicates N6-methyladenosine(m6A)modification in ALS pathogenesis.Methylated RNA immunoprecipitatio...Amyotrophic lateral sclerosis(ALS)is a progressive neurogenerative disorder with uncertain origins.Emerging evidence implicates N6-methyladenosine(m6A)modification in ALS pathogenesis.Methylated RNA immunoprecipitation sequencing(MeRIP-seq)and liquid chromatography–mass spectrometry were utilized for m6A profiling in peripheral immune cells and serum proteome analysis,respectively,in patients with ALS(n=16)and controls(n=6).The single-cell transcriptomic dataset(GSE174332)of primary motor cortex was further analyzed to illuminate the biological implications of differentially methylated genes and cell communication changes.Analysis of peripheral immune cells revealed extensive RNA hypermethylation,highlighting candidate genes with differential m6A modification and expression,including C-X3-C motif chemokine receptor 1(CX3CR1).In RAW264.7 macrophages,disrupted CX3CR1 signaling affected chemotaxis,potentially influencing immune cell migration in ALS.Serum proteome analysis demonstrated the role of dysregulated immune cell migration in ALS.Cell type-specific expression variations of these genes in the central nervous system(CNS),particularly microglia,were observed.Intercellular communication between neurons and glial cells was selectively altered in ALS CNS.This integrated approach underscores m6A dysregulation in immune cells as a potential ALS contributor.展开更多
N^6-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 previo...N^6-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 P-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 fromβ-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.展开更多
The biological functions of the epitranscriptomic modification N^(6)-methyladenosine(m^(6)A)in plants are not fully understood.CPSF30-L is a predominant isoform of the polyadenylation factor CPSF30 and consists of CPS...The biological functions of the epitranscriptomic modification N^(6)-methyladenosine(m^(6)A)in plants are not fully understood.CPSF30-L is a predominant isoform of the polyadenylation factor CPSF30 and consists of CPSF30-S and an m^(6)A-binding YTH domain.Little is known about the biological roles of CPSF30-L and the molecular mechanism underlying its m^(6)A-binding function in alternative polyadenylation.Here,we charac-terized CPSF30-L as an Arabidopsis m^(6)A reader whose m^(6)A-binding function is required for the floral tran-sition and abscisic acid(ABA)response.We found that the m^(6)A-binding activity of CPSF30-L enhances the formation of liquid-like nuclear bodies,where CPSF30-L mainly recognizes m*A-modified far-upstream elements to control polyadenylation site choice.Deficiency of CPSF30-L lengthens the 3'untranslated region of three phenotypes-related transcripts,thereby accelerating their mRNA degradation and leading to late flowering and ABA hypersensitivity.Collectively,this study uncovers a new molecular mechanism for m^(6)A-driven phase separation and polyadenylation in plants.展开更多
N6-Methyladenosine(m6 A) modification is the most pervasive modification of human mRNA molecules. It is reversible via regulation of m6 A modification methyltransferase, demethylase and proteins that preferentially re...N6-Methyladenosine(m6 A) modification is the most pervasive modification of human mRNA molecules. It is reversible via regulation of m6 A modification methyltransferase, demethylase and proteins that preferentially recognize m6 A modification as "writers", "erasers" and "readers", respectively. Altered expression levels of the m6 A modification key regulators substantially affect their function, leading to significant phenotype changes in the cell and organism. Recent studies have proved that the m6 A modification plays significant roles in regulation of metabolism, stem cell self-renewal, and metastasis in a variety of human cancers. In this review, we describe the potential roles of m6 A modification in human cancers and summarize their underlying molecular mechanisms. Moreover, we will highlight potential therapeutic approaches by targeting the key m6 A modification regulators for cancer drug development.& 2018 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license(http://creativecommons.org/licenses/by-nc-nd/4.0/).展开更多
N6-methyladenosine(m6A)represents the most abundantly occurring m RNA modification and is involved in the regulation of skeletal muscle development.However,the status and function of m6A methylation in prenatal myogen...N6-methyladenosine(m6A)represents the most abundantly occurring m RNA modification and is involved in the regulation of skeletal muscle development.However,the status and function of m6A methylation in prenatal myogenesis remains unclear.In this study,we first demonstrated that knockdown of METTL14,an m6A methyltransferase,inhibited the differentiation and promoted the proliferation of C2 C12 myoblast cells.Then,using a refined m6A-specific methylated RNA immunoprecipitation(RIP)with next generation sequencing(Me RIP-seq)method that is optimal for use with samples containing small amounts of RNA,we performed transcriptome-wide m6A profiling for six prenatal skeletal muscle developmental stages spanning two important waves of porcine myogenesis.The results revealed that,along with a continuous decrease in the m RNA expression of the m6A reader protein insulin-like growth factor 2 m RNA-binding protein 1(IGF2 BP1),the m6A methylome underwent highly dynamic changes across different development stages,with most of the affected genes being enriched in pathways related to skeletal muscle development.RNA immunoprecipitation confirmed that IGF2 BP1 targets 76 genes involved in pathways associated with muscle development,including the key marker genes MYH2 and Myo G.Moreover,small interfering RNA(si RNA)-mediated knockdown of IGF2 BP1 induced phenotypic changes in C2C12 myoblasts similar to those observed with knockdown of METTL14.In conclusion,we clarified the dynamics of m6A methylation and identified key genes involved in the regulatory network of porcine skeletal muscle development.展开更多
As the most prevalent and abundant transcriptional modification in the eukaryotic genome,the continuous and dynamic regulation of N^6-methyladenosine(m^6 A)has been shown to play a vital role in physiological and path...As the most prevalent and abundant transcriptional modification in the eukaryotic genome,the continuous and dynamic regulation of N^6-methyladenosine(m^6 A)has been shown to play a vital role in physiological and pathological processes of cardiovascular diseases(CVDs),such as ischemic heart failure(HF),myocardial hypertrophy,myocardial infarction(MI),and cardiomyogenesis.Regulation is achieved by modulating the expression of m^6 A enzymes and their downstream cardiac genes.In addition,this process has a major impact on different aspects of internal biological metabolism and several other external environmental effects associated with the development of CVDs.However,the exact molecular mechanism of m^6 A epigenetic regulation has not been fully elucidated.In this review,we outline recent advances and discuss potential therapeutic strategies for managing m^6 A in relation to several common CVD-related metabolic disorders and external environmental factors.Note that an appropriate understanding of the biological function of m^6 A in the cardiovascular system will pave the way towards exploring the mechanisms responsible for the development of other CVDs and their associated symptoms.Finally,it can provide new insights for the development of novel therapeutic agents for use in clinical practice.展开更多
Liver cancer is highly heterogeneous,and the tumor tissue harbors a variety of cell types.Liver tumor initiating cells(TICs)well contribute to tumor heterogeneity and account for tumor initiation and metastasis,but th...Liver cancer is highly heterogeneous,and the tumor tissue harbors a variety of cell types.Liver tumor initiating cells(TICs)well contribute to tumor heterogeneity and account for tumor initiation and metastasis,but the molecular mechanisms of liver TIC self-renewal are elusive.Here,we identified a functional read-through rt-circRNA,termed rtcisE2F,that is highly expressed in liver cancer and liver TICs.rtcisE2F plays essential roles in the self-renewal and activities of liver TICs.rtcisE2F targets E2F6 and E2F3 mRNAs,attenuates mRNA turnover,and increases E2F6/E2F3 expression.Mechanistically,rtcisE2F functions as a scaffold of N^(6)-methyladenosine(m^(6)A)reader IGF2BP2 and E2F6/E2F3 mRNA.rtcisE2F promotes the association of E2F6/E2F3 mRNAs with IGF2BP2,and inhibits their association with another m^(6)A reader,YTHDF2.IGF2BP2 inhibits E2F6/E2F3 mRNA decay,whereas YTHDF2 promotes E2F6/E2F3 mRNA decay.By switching m^(6)A readers,rtcisE2F enhances E2F6/E2F3 mRNA stability.E2F6 and E2F3 are both required for liver TIC self-renewal and Wnt/β-catenin activation,and inhibition of these pathways is a potential strategy for preventing liver tumorigenesis and metastasis.In conclusion,the rtcisE2F-IGF2BP2/YTHDF2-E2F6/E2F3-Wnt/β-catenin axis drives liver TIC self-renewal and initiates liver tumorigenesis and metastasis,and may provide a strategy to eliminate liver TICs.展开更多
RNA modifications are abundant in eukaryotes, bacteria, and archaea. N^6-methyladenosine(m^6A), a type of RNA modification mainly found in messenger RNA(mRNA), has significant effects on the metabolism and function of...RNA modifications are abundant in eukaryotes, bacteria, and archaea. N^6-methyladenosine(m^6A), a type of RNA modification mainly found in messenger RNA(mRNA), has significant effects on the metabolism and function of m RNAs. This modification is governed by three types of proteins, namely methyltransferases as ‘‘writers' ', demethylases as ‘‘erasers' ',and specific m^6A-binding proteins(YTHDF1-3) as ‘‘readers' '. Further, it is important for the regulation of cell fate and has a critical function in many biological processes including virus replication, stem cell differentiation, and cancer development, and exerts its effect by controlling gene expression. Herein, we summarize recent advances in research on m^6A in virus replication and T cell regulation, which is a rapidly emerging field that will facilitate the development of antiviral therapies and the study of innate immunity.展开更多
RNA N^(6)-methyladenosine modification is the most prevalent internal modification of eukaryotic RNAs and has emerged as a novel field of RNA epigenetics,garnering increased attention.To date,m^(6)A modification has b...RNA N^(6)-methyladenosine modification is the most prevalent internal modification of eukaryotic RNAs and has emerged as a novel field of RNA epigenetics,garnering increased attention.To date,m^(6)A modification has been shown to impact multiple RNA metabolic processes and play a vital role in numerous biological processes.Recent evidence suggests that aberrant m^(6)A modification is a hallmark of cancer,and it plays a critical role in cancer development and progression through multiple mechanisms.Here,we review the biological functions of mRNA m^(6)A modification in various types of cancers,with a particular focus on metabolic reprogramming,programmed cell death and tumor metastasis.Furthermore,we discuss the potential of targetingm^(6)Amodification or its regulatory proteins as a novel approach of cancer therapy and the progress of research on m^(6)A modification in tumor immunity and immunotherapy.Finally,we summarize the development of different m^(6)A detection methods and their advantages and disadvantages.展开更多
N^(6)-methyladenosine(m^(6)A)RNA is the most abundant modification of mRNA,and has been demonstrated in regulating various post-transcriptional processes.Many studies have shown that m^(6)A methylation plays key roles...N^(6)-methyladenosine(m^(6)A)RNA is the most abundant modification of mRNA,and has been demonstrated in regulating various post-transcriptional processes.Many studies have shown that m^(6)A methylation plays key roles in sex determination,neuronal functions,and embryonic development in Drosophila and mammals.Here,we analyzed transcriptome-wide profile of m^(6)A modification in the embryonic development of the destructive agricultural pest Spodoptera frugiperda.We found that the 2 key mRNA m^(6)A methyltransferases SfrMETTL3 and SfrMETTL14 have high homologies with other insects and mammals,suggesting that SfrMETTL3 and SfrMETTL14 may have conserved function among different species.From methylated RNA immunoprecipitation sequencing analysis,we obtained 46869 m^(6)A peaks representing 8587 transcripts in the 2-h embryos after oviposition,and 41389 m^(6)A peaks representing 9230 transcripts in the 24-h embryos.In addition,5995 m^(6)A peaks were differentially expressed including 3752 upregulated and 2243 downregulated peaks.Functional analysis with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes suggested that differentially expressed m^(6)A peak-modified genes were enriched in cell and organ development between the 2-and 24-h embryos.By conjoint analysis of methylated RNA immunoprecipitation-seq and RNA-seq data,we found that RNA m^(6)A methylation may regulate the transcriptional levels of genes related to tissue and organ development from 2-to 24-h embryos.Our study reveals the role of RNA m^(6)A epigenetic regulation in the embryonic development of S.frugiperda,and provides new insights for the embryonic development of insects.展开更多
基金supported in part by the National Natural Science Foundation of China(62373348)the Natural Science Foundation of Xinjiang Uygur Autonomous Region(2021D01D05)+1 种基金the Tianshan Talent Training Program(2023TSYCLJ0021)the Pioneer Hundred Talents Program of Chinese Academy of Sciences.
文摘N6-methyladenosine(m6A)is an important RNA methylation modification involved in regulating diverse biological processes across multiple species.Hence,the identification of m6A modification sites provides valuable insight into the biological mechanisms of complex diseases at the post-transcriptional level.Although a variety of identification algorithms have been proposed recently,most of them capture the features of m6A modification sites by focusing on the sequential dependencies of nucleotides at different positions in RNA sequences,while ignoring the structural dependencies of nucleotides in their threedimensional structures.To overcome this issue,we propose a cross-species end-to-end deep learning model,namely CR-NSSD,which conduct a cross-domain representation learning process integrating nucleotide structural and sequential dependencies for RNA m6A site identification.Specifically,CR-NSSD first obtains the pre-coded representations of RNA sequences by incorporating the position information into single-nucleotide states with chaos game representation theory.It then constructs a crossdomain reconstruction encoder to learn the sequential and structural dependencies between nucleotides.By minimizing the reconstruction and binary cross-entropy losses,CR-NSSD is trained to complete the task of m6A site identification.Extensive experiments have demonstrated the promising performance of CR-NSSD by comparing it with several state-of-the-art m6A identification algorithms.Moreover,the results of cross-species prediction indicate that the integration of sequential and structural dependencies allows CR-NSSD to capture general features of m6A modification sites among different species,thus improving the accuracy of cross-species identification.
基金the Joint Funds for the Innovation of Science and Technology Program of Fujian Province,China(2018Y9110)the Natural Science Foundation of Fujian Province,China,(2020J011126)the China Postdoctoral Science Foundation(2021T140468).
文摘Background:Stemness and chemoresistance contribute to cervical cancer recurrence and metastasis.In the current study,we determined the relevant players and role of N^(6)-methyladenine(m^(6)A)RNA methylation in cervical cancer progression.Methods:The roles of m^(6)A RNA methylation and centromere protein K(CENPK)in cervical cancer were analyzed using bioinformatics analysis.Methylated RNA immunoprecipitation was adopted to detect m^(6)A modification of CENPK mRNA.Human cervical cancer clinical samples,cell lines,and xenografts were used for analyzing gene expression and function.Immunofluorescence staining and the tumorsphere formation,clonogenic,MTT,and EdU assays were performed to determine cell stemness,chemoresistance,migration,invasion,and proliferation in HeLa and SiHa cells,respectively.Western blot analysis,co-immunoprecipitation,chromatin immunoprecipitation,and luciferase reporter,cycloheximide chase,and cell fractionation assays were performed to elucidate the underlying mechanism.Results:Bioinformatics analysis of public cancer datasets revealed firm links between m^(6)A modification patterns and cervical cancer prognosis,especially through ZC3H13-mediated m^(6)A modification of CENPK mRNA.CENPK expression was elevated in cervical cancer,associated with cancer recurrence,and independently predicts poor patient prognosis[hazard ratio=1.413,95%confidence interval=1.078−1.853,P=0.012].Silencing of CENPK prolonged the overall survival time of cervical cancer-bearing mice and improved the response of cervical cancer tumors to chemotherapy in vivo(P<0.001).We also showed that CENPK was directly bound to SOX6 and disrupted the interactions of CENPK withβ-catenin,which promotedβ-catenin expression and nuclear translocation,facilitated p53 ubiquitination,and led to activation of Wnt/β-catenin signaling,but suppression of the p53 pathway.This dysregulation ultimately enhanced the tumorigenic pathways required for cell stemness,DNA damage repair pathways necessary for cisplatin/carboplatin resistance,epithelial-mesenchymal transition involved in metastasis,and DNA replication that drove tumor cell proliferation.Conclusions:CENPK was shown to have an oncogenic role in cervical cancer and can thus serve as a prognostic indicator and novel target for cervical cancer treatment.
基金This research was supported by grants from the National Natural Science Foundation of China(Grant Nos.81922052,81974435,and 81772999)Natural Science Foundation of Guangdong Province(Grant No.2019B151502011)the Guangzhou People’s Livelihood Science and Technology Project(Grant No.201903010006).
文摘Growing evidence supports that cancer progression is closely associated with the tumor microenvironment and immune evasion.Importantly,recent studies have revealed the crucial roles of epigenetic regulators in shaping the tumor microenvironment and restoring immune recognition.N^(6)-methyladenosine(m^(6)A)modification,the most prevalent epigenetic modification of mammalian mRNAs,has essential functions in regulating the processing and metabolism of its targeted RNAs,and therefore affects various biological processes including tumorigenesis and progression.Recent studies have demonstrated the critical functions and molecular mechanisms underlying abnormal m^(6)A modification in the regulation of tumor immunity.In this review,we summarize recent research progress in the potential roles of m^(6)A modification in tumor immunoregulation,with a special focus on the anti-tumor processes of immune cells and involvement in immune-associated molecules and pathways.Furthermore,we review current knowledge regarding the close correlation between m6A-related risk signatures and the tumor immune microenvironment landscape,and we discuss the prognostic value and therapeutic efficacy of m^(6)A regulators in a variety of cancer types.
基金Supported by Project of Shanghai Science and Technology (No.20ZR1443600)。
文摘N6-methyladenosine(m6A)modification is a reversible process promoted by“writers”,inhibited by“erasers”,and processed by“readers”.During the last decade,increasing emphasis has been placed on the underlying roles of m6A modification owing to their great importance in biological significance.The abnormal regulation of m6A modification will lead to aberrant cellular behavior and various diseases.Recently,studies have demonstrated that m6A modification is closely associated with the genesis and progression of ocular surface diseases(OSDs).This review focus on the role of m6A modification and research progress in OSDs including fungal keratitis,herpes simplex keratitis,immunerelated keratoconjunctival diseases,pterygium,ocular chemical burns,and Graves’ophthalmopathy,which may provide new insights into and prospective applications for OSDs.
基金the Natural Science Foundation of Zhejiang province(Grant Nos.LQ23C150003,LR23C150001)the National Natural Science Foundation of China(NSFC)(Grant No.32102318)NSFC Excellent Young Scientists Fund.
文摘N6-methyladenosine(m^(6)A)RNA modification is a conserved mechanism that regulates the fate of RNA across eukaryotic organisms.Despite its significance,a comprehensive analysis of m^(6)A-related genes in non-model plants,such as kiwifruit,is lacking.Here,we identified 36 m^(6)A-related genes in the kiwifruit genome according to homology and phylogenetic inference.We performed bioinformatics and evolutionary analyses of the writer,eraser,and reader families of m^(6)A modification.Reanalysis of public RNA-seq data collected from samples under various biotic and abiotic stresses indicated that most m^(6)A-related genes were remarkably expressed under different conditions.Through construction of gene co-expression networks,we found significant correlations between several m^(6)A-related genes and transcription factors(TFs)as well as receptor-like genes during the development and ripening of kiwifruit.Furthermore,we performed ATAC-seq assays on diverse kiwifruit tissues to investigate the regulatory mechanisms of m^(6)A-related genes.We identified 10 common open chromatin regions that were present in at least two tissues,and these regions might serve as potential binding sites for MADS protein,C2H2 protein,and other predicted TFs.Our study offers comprehensive insights into the gene family of m^(6)A-related components in kiwifruit,which will lay foundation for exploring mechanisms of post-transcriptional regulation involved in development and adaptation of kiwifruit.
基金Justin Jong-Leong Wong holds a Fellowship from the Cancer Institute of NSW and receives funding from the National Health and Medical Research Council of Australia (Grant No 1128175, 1129901 and 1126306)
文摘N^6-methyladenosine(m^6 A) is an essential RNA modification that regulates key cellular processes, including stem cell renewal,cellular differentiation, and response to DNA damage. Unsurprisingly, aberrant m^6 A methylation has been implicated in the development and maintenance of diverse human cancers. Altered m^6 A levels affect RNA processing, mRNA degradation, and translation of mRNAs into proteins, thereby disrupting gene expression regulation and promoting tumorigenesis. Recent studies have reported that the abnormal expression of m^6 A regulatory enzymes affects m^6 A abundance and consequently dysregulates the expression of tumor suppressor genes and oncogenes, including MYC, SOCS2, ADAM19, and PTEN. In this review, we discuss the specific roles of m^6 A missing space "writers", "erasers", and "readers" in normal physiology and how their altered expression promotes tumorigenesis. We also describe the potential of exploiting the aberrant expression of these enzymes for cancer diagnosis, prognosis, and the development of novel therapies.
基金supported by the National Natural Science Foundation of China(Grant No.81772621)the National Key R&D Program of China(Grant No.2017YFA0504400).
文摘Objective:Investigation of the regulatory mechanisms of cell stemness in cholangiocarcinoma(CCA)is essential for developing effective therapies to improve patient outcomes.The purpose of this study was to investigate the function and regulatory mechanism of m6A modifications in CCA cell stemness.Methods:Interleukin 6(IL-6)treatment was used to induce an inflammatory response,and loss-of-function studies were conducted using mammosphere culture assays.Chromatin immunoprecipitation,polysome profiling,and methylated RNA immunoprecipitation analyses were used to identify signaling pathways.The in vitro findings were verified in a mice model.Results:We first identified that m6A writers were highly expressed in CCAs and further showed that STAT3 directly bound to the gene loci of m6A writers,showing that IL-6/STAT3 signaling regulated expressions of m6A writers.Downregulating m6A writers prevented cell proliferation and migration in vitro and suppressed CCA tumorigenesis in vivo.Notably,the knockdown of m6A writers inhibited CCA cell stemness that was triggered by IL-6 treatment.Mechanistically,IGF2BP2 was bound to CTNNB1 transcripts,significantly enhancing their stability and translation,and conferring stem-like properties.Finally,we confirmed that the combination of m6A writers,IGF2BP2,and CTNNB1 distinguished CCA tissues from normal tissues.Conclusions:Overall,this study showed that the IL-6-triggered inflammatory response facilitated the expressions of m6A writers and cell stemness in an m6A-IGF2BP2-dependent manner.Furthermore,the study showed that m6A modification was a targetable mediator of the response to inflammation factor exposure,was a potential diagnostic biomarker for CCA,and was critical to the progression of CCA.
文摘Background and Objective N6-methyladenosine(m6A)plays critical roles in many fundamental biological processes and a variety of diseases.The aim of this study was to investigate the effect of the m6ASNPs on lipid levels.Methods We examined the association of m6A-SNPs with lipid levels in a GWAS of 188,578 individuals.Furthermore,we performed eQTL and differential expression analyses to add additional information for the identified m6A-SNPs.
文摘N^(6)-甲基腺嘌呤(N6-methyladenine,m^(6)A)修饰作为信使RNA中广泛存在的一种甲基化修饰,它的动态变化在生命活动和疾病的发生发展中发挥着重要的作用。近年来研究发现,通过改变靶基因的m6A修饰水平可以调控肿瘤的进展,因此,通过小分子靶向干预m^(6)A去甲基化酶可作为抗肿瘤的新策略。本文重点讨论了m^(6)A去甲基化酶,包括脂肪含量与肥胖相关蛋白(fat mass and obesity-associated protein,FTO)和AlkB同源蛋白5(AlkB homlog5,ALKBH5)的作用方式以及它们在肿瘤中发挥的生物学功能,并总结了m^(6)A去甲基化酶小分子抑制剂的研究进展。
基金supported by the Strategic Priority Research Program(Pilot study)“Biological basis of aging and therapeutic strategies”of the Chinese Academy of Sciences(No.XDB39040000)CAMS Innovation Fund for Medical Sciences(Nos.2021-I2M-1-003 and 2021-I2M-1-034)+2 种基金National High Level Hospital Clinical Research Funding(No.2022-PUMCH-B-017)Beijing Natural Science Foundation(No.7202158)National Natural Science Foundation of China(No.81971293).
文摘Amyotrophic lateral sclerosis(ALS)is a progressive neurogenerative disorder with uncertain origins.Emerging evidence implicates N6-methyladenosine(m6A)modification in ALS pathogenesis.Methylated RNA immunoprecipitation sequencing(MeRIP-seq)and liquid chromatography–mass spectrometry were utilized for m6A profiling in peripheral immune cells and serum proteome analysis,respectively,in patients with ALS(n=16)and controls(n=6).The single-cell transcriptomic dataset(GSE174332)of primary motor cortex was further analyzed to illuminate the biological implications of differentially methylated genes and cell communication changes.Analysis of peripheral immune cells revealed extensive RNA hypermethylation,highlighting candidate genes with differential m6A modification and expression,including C-X3-C motif chemokine receptor 1(CX3CR1).In RAW264.7 macrophages,disrupted CX3CR1 signaling affected chemotaxis,potentially influencing immune cell migration in ALS.Serum proteome analysis demonstrated the role of dysregulated immune cell migration in ALS.Cell type-specific expression variations of these genes in the central nervous system(CNS),particularly microglia,were observed.Intercellular communication between neurons and glial cells was selectively altered in ALS CNS.This integrated approach underscores m6A dysregulation in immune cells as a potential ALS contributor.
文摘N^6-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 P-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 fromβ-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.
基金This work was supported by the National Natural Science Foundation of China(nos.21822702,21820102008,92053109,and 21432002)the National Basic Research Program of China(2017YFA0505201 and 2019YFA0802201).
文摘The biological functions of the epitranscriptomic modification N^(6)-methyladenosine(m^(6)A)in plants are not fully understood.CPSF30-L is a predominant isoform of the polyadenylation factor CPSF30 and consists of CPSF30-S and an m^(6)A-binding YTH domain.Little is known about the biological roles of CPSF30-L and the molecular mechanism underlying its m^(6)A-binding function in alternative polyadenylation.Here,we charac-terized CPSF30-L as an Arabidopsis m^(6)A reader whose m^(6)A-binding function is required for the floral tran-sition and abscisic acid(ABA)response.We found that the m^(6)A-binding activity of CPSF30-L enhances the formation of liquid-like nuclear bodies,where CPSF30-L mainly recognizes m*A-modified far-upstream elements to control polyadenylation site choice.Deficiency of CPSF30-L lengthens the 3'untranslated region of three phenotypes-related transcripts,thereby accelerating their mRNA degradation and leading to late flowering and ABA hypersensitivity.Collectively,this study uncovers a new molecular mechanism for m^(6)A-driven phase separation and polyadenylation in plants.
基金supported in part by a grant from the National Natural Science Foundation of China (No. 31701114)the Fundamental Research Funds for University-Key Cultivation Project of Young Teacher in Sun Yat-Sen University (No. 17ykzd11)
文摘N6-Methyladenosine(m6 A) modification is the most pervasive modification of human mRNA molecules. It is reversible via regulation of m6 A modification methyltransferase, demethylase and proteins that preferentially recognize m6 A modification as "writers", "erasers" and "readers", respectively. Altered expression levels of the m6 A modification key regulators substantially affect their function, leading to significant phenotype changes in the cell and organism. Recent studies have proved that the m6 A modification plays significant roles in regulation of metabolism, stem cell self-renewal, and metastasis in a variety of human cancers. In this review, we describe the potential roles of m6 A modification in human cancers and summarize their underlying molecular mechanisms. Moreover, we will highlight potential therapeutic approaches by targeting the key m6 A modification regulators for cancer drug development.& 2018 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license(http://creativecommons.org/licenses/by-nc-nd/4.0/).
基金supported by the Agricultural Science and Technology Innovation ProgramThe Elite Young Scientists Program of CAAS+3 种基金supported by the National Natural Science Foundation of China(31830090)the National Key Project(2016ZX08009003-006)the Shenzhen Dapeng New District Special Fund for Industry Development(KY20180114)the Agricultural Science and Technology Innovation Program(ASTIP-AGIS5)
文摘N6-methyladenosine(m6A)represents the most abundantly occurring m RNA modification and is involved in the regulation of skeletal muscle development.However,the status and function of m6A methylation in prenatal myogenesis remains unclear.In this study,we first demonstrated that knockdown of METTL14,an m6A methyltransferase,inhibited the differentiation and promoted the proliferation of C2 C12 myoblast cells.Then,using a refined m6A-specific methylated RNA immunoprecipitation(RIP)with next generation sequencing(Me RIP-seq)method that is optimal for use with samples containing small amounts of RNA,we performed transcriptome-wide m6A profiling for six prenatal skeletal muscle developmental stages spanning two important waves of porcine myogenesis.The results revealed that,along with a continuous decrease in the m RNA expression of the m6A reader protein insulin-like growth factor 2 m RNA-binding protein 1(IGF2 BP1),the m6A methylome underwent highly dynamic changes across different development stages,with most of the affected genes being enriched in pathways related to skeletal muscle development.RNA immunoprecipitation confirmed that IGF2 BP1 targets 76 genes involved in pathways associated with muscle development,including the key marker genes MYH2 and Myo G.Moreover,small interfering RNA(si RNA)-mediated knockdown of IGF2 BP1 induced phenotypic changes in C2C12 myoblasts similar to those observed with knockdown of METTL14.In conclusion,we clarified the dynamics of m6A methylation and identified key genes involved in the regulatory network of porcine skeletal muscle development.
基金Project supported by the Grants-in-Aid from the Graduate Research and Innovation Projects of Jiangsu Province(No.KYCX18_1461),China。
文摘As the most prevalent and abundant transcriptional modification in the eukaryotic genome,the continuous and dynamic regulation of N^6-methyladenosine(m^6 A)has been shown to play a vital role in physiological and pathological processes of cardiovascular diseases(CVDs),such as ischemic heart failure(HF),myocardial hypertrophy,myocardial infarction(MI),and cardiomyogenesis.Regulation is achieved by modulating the expression of m^6 A enzymes and their downstream cardiac genes.In addition,this process has a major impact on different aspects of internal biological metabolism and several other external environmental effects associated with the development of CVDs.However,the exact molecular mechanism of m^6 A epigenetic regulation has not been fully elucidated.In this review,we outline recent advances and discuss potential therapeutic strategies for managing m^6 A in relation to several common CVD-related metabolic disorders and external environmental factors.Note that an appropriate understanding of the biological function of m^6 A in the cardiovascular system will pave the way towards exploring the mechanisms responsible for the development of other CVDs and their associated symptoms.Finally,it can provide new insights for the development of novel therapeutic agents for use in clinical practice.
基金This work was supported by the National Natural Science Foundation of China(31922024,81872411,32170874,82173176)Science Foundation for Excellent Young Scholars in Henan(202300410358).
文摘Liver cancer is highly heterogeneous,and the tumor tissue harbors a variety of cell types.Liver tumor initiating cells(TICs)well contribute to tumor heterogeneity and account for tumor initiation and metastasis,but the molecular mechanisms of liver TIC self-renewal are elusive.Here,we identified a functional read-through rt-circRNA,termed rtcisE2F,that is highly expressed in liver cancer and liver TICs.rtcisE2F plays essential roles in the self-renewal and activities of liver TICs.rtcisE2F targets E2F6 and E2F3 mRNAs,attenuates mRNA turnover,and increases E2F6/E2F3 expression.Mechanistically,rtcisE2F functions as a scaffold of N^(6)-methyladenosine(m^(6)A)reader IGF2BP2 and E2F6/E2F3 mRNA.rtcisE2F promotes the association of E2F6/E2F3 mRNAs with IGF2BP2,and inhibits their association with another m^(6)A reader,YTHDF2.IGF2BP2 inhibits E2F6/E2F3 mRNA decay,whereas YTHDF2 promotes E2F6/E2F3 mRNA decay.By switching m^(6)A readers,rtcisE2F enhances E2F6/E2F3 mRNA stability.E2F6 and E2F3 are both required for liver TIC self-renewal and Wnt/β-catenin activation,and inhibition of these pathways is a potential strategy for preventing liver tumorigenesis and metastasis.In conclusion,the rtcisE2F-IGF2BP2/YTHDF2-E2F6/E2F3-Wnt/β-catenin axis drives liver TIC self-renewal and initiates liver tumorigenesis and metastasis,and may provide a strategy to eliminate liver TICs.
基金supported by funding from the National Natural Science Foundation of China (Nos. 81672004, 31270202,81801993, and 81801994)the Jilin University Science and Technology Innovative Research Team (JLUSTIRT, 2017TD-05)+3 种基金the Science and Technology Department of Jilin Province (20160101044JC)the Health and Family Planning Commission of Jilin Province (2013Z066)the Key Laboratory of Molecular Virology, Jilin Province (20102209)China Postdocotoral Science Foundation (2018M631869)
文摘RNA modifications are abundant in eukaryotes, bacteria, and archaea. N^6-methyladenosine(m^6A), a type of RNA modification mainly found in messenger RNA(mRNA), has significant effects on the metabolism and function of m RNAs. This modification is governed by three types of proteins, namely methyltransferases as ‘‘writers' ', demethylases as ‘‘erasers' ',and specific m^6A-binding proteins(YTHDF1-3) as ‘‘readers' '. Further, it is important for the regulation of cell fate and has a critical function in many biological processes including virus replication, stem cell differentiation, and cancer development, and exerts its effect by controlling gene expression. Herein, we summarize recent advances in research on m^6A in virus replication and T cell regulation, which is a rapidly emerging field that will facilitate the development of antiviral therapies and the study of innate immunity.
基金supported by the National Key R&D Program of China(2021YFA1302100)Natural Science Foundation of China(82072617 to J.Zheng,82003162 to J.Zhang)+1 种基金Program for Guangdong Introducing Innovative and Entrepreneurial Teams(2017ZT07S096 to D.L.)Sun Yat-sen University Intramural Funds(to D.L.and to J.Zheng).
文摘RNA N^(6)-methyladenosine modification is the most prevalent internal modification of eukaryotic RNAs and has emerged as a novel field of RNA epigenetics,garnering increased attention.To date,m^(6)A modification has been shown to impact multiple RNA metabolic processes and play a vital role in numerous biological processes.Recent evidence suggests that aberrant m^(6)A modification is a hallmark of cancer,and it plays a critical role in cancer development and progression through multiple mechanisms.Here,we review the biological functions of mRNA m^(6)A modification in various types of cancers,with a particular focus on metabolic reprogramming,programmed cell death and tumor metastasis.Furthermore,we discuss the potential of targetingm^(6)Amodification or its regulatory proteins as a novel approach of cancer therapy and the progress of research on m^(6)A modification in tumor immunity and immunotherapy.Finally,we summarize the development of different m^(6)A detection methods and their advantages and disadvantages.
基金supported by China Postdoctoral Science Foundation(2021M691094)the National Natural Science Foundation of China(32070615,81902093)+3 种基金Guangdong Provincial Natural Science Foundation(2021A1515010823 and 2022A1515010569)Guangzhou Science and Technology Project(202002030100)Guangdong Provincial Science and Technology Agricultural Program(KTP20200105)Guangdong Province Universities and Colleges Pearl River Scholar Funded Scheme to XYW.We thank the National Center for Protein Sciences at Peking University and Hui Li for assistance with the LC-MS/MS quantification of m^(6)A levels.
文摘N^(6)-methyladenosine(m^(6)A)RNA is the most abundant modification of mRNA,and has been demonstrated in regulating various post-transcriptional processes.Many studies have shown that m^(6)A methylation plays key roles in sex determination,neuronal functions,and embryonic development in Drosophila and mammals.Here,we analyzed transcriptome-wide profile of m^(6)A modification in the embryonic development of the destructive agricultural pest Spodoptera frugiperda.We found that the 2 key mRNA m^(6)A methyltransferases SfrMETTL3 and SfrMETTL14 have high homologies with other insects and mammals,suggesting that SfrMETTL3 and SfrMETTL14 may have conserved function among different species.From methylated RNA immunoprecipitation sequencing analysis,we obtained 46869 m^(6)A peaks representing 8587 transcripts in the 2-h embryos after oviposition,and 41389 m^(6)A peaks representing 9230 transcripts in the 24-h embryos.In addition,5995 m^(6)A peaks were differentially expressed including 3752 upregulated and 2243 downregulated peaks.Functional analysis with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes suggested that differentially expressed m^(6)A peak-modified genes were enriched in cell and organ development between the 2-and 24-h embryos.By conjoint analysis of methylated RNA immunoprecipitation-seq and RNA-seq data,we found that RNA m^(6)A methylation may regulate the transcriptional levels of genes related to tissue and organ development from 2-to 24-h embryos.Our study reveals the role of RNA m^(6)A epigenetic regulation in the embryonic development of S.frugiperda,and provides new insights for the embryonic development of insects.