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Learning Sequential and Structural Dependencies Between Nucleotides for RNA N6-Methyladenosine Site Identification
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作者 Guodong Li Bowei Zhao +4 位作者 Xiaorui Su Dongxu Li Yue Yang Zhi Zeng Lun Hu 《IEEE/CAA Journal of Automatica Sinica》 SCIE EI CSCD 2024年第10期2123-2134,共12页
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
关键词 Cross-domain reconstruction cross-species prediction N6-methyladenosine(m6a)modification site RNA sequence sequential and structural dependencies
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N^(6)-methyladenosine modification of CENPK mRNA by ZC3H13 promotes cervical cancer stemness and chemoresistance 被引量:6
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作者 Xian Lin Feng Wang +5 位作者 Jian Chen Jing Liu Yi-Bin Lin Li Li Chuan-Ben Chen Qin Xu 《Military Medical Research》 SCIE CAS CSCD 2022年第5期576-591,共16页
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
关键词 N^(6)-methyladenosine Centromere protein K Cervical cancer STEmNESS CHEmORESISTANCE
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N^(6)-methyladenosine(m^(6)A)RNA modification in tumor immunity
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作者 Siyi Zheng Hui Han Shuibin Lin 《Cancer Biology & Medicine》 SCIE CAS CSCD 2022年第4期385-397,共13页
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
关键词 N^(6)-methyladenosine(m^(6)A)modification immune evasion tumor microenvironment(TmE) tumor immunology immune cells
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Recent progress in N6-methyladenosine modification in ocular surface diseases 被引量:2
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作者 Wei Wang Jun Zou 《International Journal of Ophthalmology(English edition)》 SCIE CAS 2023年第4期645-651,共7页
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
关键词 N6-methyladenosine m6a modification EPIGENETICS ocular surface diseases
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m^(6)A修饰在病毒感染宿主细胞中的调节作用
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作者 夏月平 黄芬 《中国生物化学与分子生物学报》 CAS CSCD 北大核心 2024年第10期1362-1373,共12页
N^(6)-甲基腺苷(N^(6)-methyladenosine,m^(6)A)是指RNA分子腺嘌呤第6位氮原子上发生的甲基化修饰,是信使RNA(mRNA)和非编码RNA(ncRNA)中最常见的转录后修饰。m^(6)A修饰在RNA循环的所有阶段,包括RNA稳定、剪接、核输出、折叠、翻译和... N^(6)-甲基腺苷(N^(6)-methyladenosine,m^(6)A)是指RNA分子腺嘌呤第6位氮原子上发生的甲基化修饰,是信使RNA(mRNA)和非编码RNA(ncRNA)中最常见的转录后修饰。m^(6)A修饰在RNA循环的所有阶段,包括RNA稳定、剪接、核输出、折叠、翻译和降解等过程中发挥重要作用,这一过程需甲基转移酶(writers)、去甲基酶(erasers)和m^(6)A阅读蛋白(readers)的参与。随着RNA高通量测序技术的不断发展,m^(6)A修饰参与病毒与宿主互作中的研究不断涌现。研究表明m^(6)A修饰发生在多种RNA病毒中,影响病毒感染、复制及子代病毒粒子的生成。病毒也可通过改变宿主细胞转录物组的m^(6)A修饰影响病毒的感染性或宿主对病毒的抵抗性。本文对呼吸道病毒、反转录病毒、疱疹病毒等感染宿主细胞造成的m^(6)A修饰进行概述,并针对m^(6)A修饰对病毒的复制及对宿主免疫反应的调节作用进行综述,为了解病毒与宿主互作机制研究及抗病毒药物筛选供理论基础。 展开更多
关键词 N^(6)-methyladenosine(m^(6)A) m^(6)A甲基转移酶 m^(6)A去甲基酶 m^(6)A阅读蛋白 病毒
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Identification and characterization of genes related to m^(6)A modification in kiwifruit using RNA-seq and ATAC-seq
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作者 Xiaoli Hu Tong Li +6 位作者 Changbin Xu Yanna Xu Congjun You Xinyi Li Jinli Gong Xiaolong Li Xuepeng Sun 《Horticultural Plant Journal》 SCIE CAS CSCD 2024年第5期1121-1133,共13页
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
关键词 KIWIFRUIT N^(6)-methyladenosine Phylogenetic analysis CIS-ELEmENT Co-expression network
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Aberrant expression of enzymes regulating m^6A mRNA methylation: implication in cancer 被引量:17
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作者 Natalia Pinello Stephanie Sun Justin Jong-Leong Wong 《Cancer Biology & Medicine》 SCIE CAS CSCD 2018年第4期323-334,共12页
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
关键词 RNA modification N^6-methyladenosine (m^6a) CANCER tumor SUPPRESSOR ONCOGENE
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The m6A writers regulated by the IL-6/STAT3 inflammatory pathway facilitate cancer cell stemness in cholangiocarcinoma
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作者 Hua Ye Tianqi Chen +5 位作者 Zhancheng Zeng Bo He Qianqian Yang Qi Pan Yueqin Chen Wentao Wang 《Cancer Biology & Medicine》 SCIE CAS CSCD 2022年第3期343-357,共15页
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
关键词 CHOLANGIOCARCINOmA IL-6 cell stemness N6-methyladenosine(m6a) IGF2BP2
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Genome-wide enrichment of m6A-associated single nucleotide polymorphisms in the lipid loci
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作者 Xingbo Mo Shufeng Lei +1 位作者 Yonghong Zhang Huan Zhang 《中国循环杂志》 CSCD 北大核心 2018年第S01期124-124,共1页
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
关键词 N6-methyladenosine(m6a) FUNDAmENTAL biological processes m6aSNPs
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N^(6)-甲基腺嘌呤去甲基化酶抑制剂研究进展
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作者 高静 米雪 +1 位作者 周琦 周君 《中国药科大学学报》 CAS CSCD 北大核心 2022年第6期663-673,共11页
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
关键词 N^(6)-甲基腺嘌呤(m6a) 去甲基化酶 脂肪含量与肥胖相关蛋白 AlkB同源蛋白5 酶抑制剂 进展
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Dysregulated N6-methyladenosine modification in peripheral immune cells contributes to the pathogenesis of amyotrophic lateral sclerosis
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作者 Di He Xunzhe Yang +5 位作者 Liyang Liu Dongchao Shen Qing Liu Mingsheng Liu Xue Zhang Liying Cui 《Frontiers of Medicine》 SCIE CSCD 2024年第2期285-302,共18页
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
关键词 amyotrophic lateral sclerosis N^(6)-methyladenosine epi-transcriptome PROTEOmE single cell RNA sequencing analysis CX3CR1
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Solution structure of the RNA recognition domain of METTL3-METTL14 N^6-methyladenosine methyltransferase 被引量:18
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作者 Jinbo Huang Xu Dong +8 位作者 Zhou Gong Ling-Yun Qin Shuai Yang Yue-Ling Zhu Xiang Wang Delin Zhang Tingting Zou Ping Yin Chun Tang 《Protein & Cell》 SCIE CAS CSCD 2019年第4期272-284,共13页
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
关键词 RNA modification N^6-methyladenosine mETTL3 target recognition DOmAIN zinc FINGER PARAmAGNETIC RELAXATION enhancement
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Arab/c/opste N^(6)-methyladenosine reader CPSF30-L recognizes FUE signals to control polyadenylation site choice in liquid-like nuclear bodies 被引量:21
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作者 Peizhe Song Junbo Yang +4 位作者 Chunling Wang Qiang Lu Linqing Shi Subiding Tayier Guifang Jia 《Molecular Plant》 SCIE CAS CSCD 2021年第4期571-587,共17页
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
关键词 epitranscriptomics N^(6)-methyladenosine(m^(6)A) m^(6)A reader CPSF30-L phase separation alternative polyadenylation(APA)
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N^6-Methyladenosine modification: a novel pharmacological target for anti-cancer drug development 被引量:8
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作者 Yi Niu Arabella Wan +2 位作者 Ziyou Lin Xiongbin Lu Guohui Wan 《Acta Pharmaceutica Sinica B》 SCIE CAS CSCD 2018年第6期833-843,共11页
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
关键词 N^6-methyladenosine Human cancer PHARmACOLOGICAL TARGET m^6a mODIFICATION REGULATOR Drug development
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Longitudinal epitranscriptome profiling reveals the crucial role of N^(6)-methyladenosine methylation in porcine prenatal skeletal muscle development 被引量:9
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作者 Xinxin Zhang Yilong Yao +4 位作者 Jinghua Han Yalan Yang Yun Chen Zhonglin Tang Fei Gao 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2020年第8期465-476,共12页
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
关键词 N^(6)-methyladenosine IGF2BP1 mYOBLAST Skeletal muscle
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Epigenetic role of N^6-methyladenosine(m^6A)RNA methylation in the cardiovascular system 被引量:6
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作者 Kun ZHAO Chuan-xi YANG +2 位作者 Peng LI Wei SUN Xiang-qing KONG 《Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)》 SCIE CAS CSCD 2020年第7期509-523,共15页
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
关键词 N^6-methyladenosine(m^6a) RNA methylation Cardiovascular system metabolic disorder
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rtcisE2F promotes the self-renewal and metastasis of liver tumorinitiating cells via N^(6)-methyladenosine-dependent E2F3/E2F6 mRNA stability 被引量:4
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作者 Zhenzhen Chen Lan Huang +5 位作者 Kaili Wang Lulu Zhang Xiang Zhong Zhongyi Yan Benyu Liu Pingping Zhu 《Science China(Life Sciences)》 SCIE CAS CSCD 2022年第9期1840-1854,共15页
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
关键词 circular RNA tumor-initiating cells SELF-RENEWAL mETASTASIS N^(6)-methyladenosine
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Regulation of Virus Replication and T Cell Homeostasis by N^6-Methyladenosine 被引量:1
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作者 Jing Yang Hong Wang Wenyan Zhang 《Virologica Sinica》 SCIE CAS CSCD 2019年第1期22-29,共8页
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
关键词 RNA mODIFICATION N^6-methyladenosine (m^6a) VIRUS REPLICATION T CELL HOmEOSTASIS
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Roles and implications of mRNA N^(6)-methyladenosine in cancer 被引量:1
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作者 Lingxing Zeng Xudong Huang +2 位作者 Jialiang Zhang Dongxin Lin Jian Zheng 《Cancer Communications》 SCIE 2023年第7期729-748,共20页
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
关键词 cancer therapy ImmUNOTHERAPY m^(6)A methylation N^(6)-methyladenosine
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Transcriptome-wide analysis of mRNA N^(6)-methyladenosine modification in the embryonic development of Spodoptera frugiperda
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作者 Yaqing Chen Yushan Lai +3 位作者 Runzhou Liu Lin Yao Xiao-Qiang Yu Xiaoyun Wang 《Insect Science》 SCIE CAS CSCD 2023年第5期1229-1244,共16页
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
关键词 embryonic cdevelopment N^(6)-methyladenosine RNA methylation Spodopterafrugiperda
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