N6-methyladenosine(m6A)is a reversible epigenetic modification, which is one of the most abundant modifiers in eukaryotic cells and has been commonly reported in messenger RNAs and non-coding RNAs. The processing modi...N6-methyladenosine(m6A)is a reversible epigenetic modification, which is one of the most abundant modifiers in eukaryotic cells and has been commonly reported in messenger RNAs and non-coding RNAs. The processing modification of m6A regulates RNA transcription, processing, splicing, degradation, and translation, and plays an important role in the biological process of tumors. Circular RNA, which lacks the 5' cap structure, has been mistakenly regarded as a "junk sequence" generated by accidental shearing during the transcription process. However, it has been found that circRNAs can be involved in tumor invasion and metastasis through microRNAs, binding proteins, translated peptides, and m6A modifications. In this paper, we reviewed the role of m6A modifications in circRNA regulation and their functions in hepatocellular carcinoma and discussed their potential clinical applications and future development in this field.展开更多
Background Intramuscular fat(IMF)content is a critical indicator of pork quality,and abnormal IMF is also relevant to human disease as well as aging.Although N6-methyladenosine(m^(6)A)RNA modification was recently fou...Background Intramuscular fat(IMF)content is a critical indicator of pork quality,and abnormal IMF is also relevant to human disease as well as aging.Although N6-methyladenosine(m^(6)A)RNA modification was recently found to regulate adipogenesis in porcine intramuscular fat,however,the underlying molecular mechanisms was still unclear.Results In this work,we collected 20 longissimus dorsi muscle samples with high(average 3.95%)or low IMF content(average 1.22%)from a unique heterogenous swine population for m^(6)A sequencing(m^(6)A-seq).We discovered 70genes show both differential RNA expression and m^(6)A modification from high and low IMF group,including ADIPOQ and SFRP1,two hub genes inferred through gene co-expression analysis.Particularly,we observed ADIPOQ,which contains three m^(6)A modification sites within 3’untranslated and protein coding region,could promote porcine intramuscular preadipocyte differentiation in an m^(6)A-dependent manner.Furthermore,we found the YT521-B homology domain family protein 1(YTHDF1)could target and promote ADIPOQ mRNA translation.Conclusions Our study provided a comprehensive profiling of m^(6)A methylation in porcine longissimus dorsi muscle and characterized the involvement of m^(6)A epigenetic modification in the regulation of ADIPOQ mRNA on IMF deposition through an m^(6)A-YTHDF1-dependent manner.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
BACKGROUND Cataracts remain a prime reason for visual disturbance and blindness all over the world,despite the capacity for successful surgical replacement with artificial lenses.Diabetic cataract(DC),a metabolic comp...BACKGROUND Cataracts remain a prime reason for visual disturbance and blindness all over the world,despite the capacity for successful surgical replacement with artificial lenses.Diabetic cataract(DC),a metabolic complication,usually occurs at an earlier age and progresses faster than age-related cataracts.Evidence has linked N6-methyladenosine(m6A)to DC progression.However,there exists a lack of understanding regarding RNA m6A modifications and the role of m6A in DC pathogenesis.AIM To elucidate the role played by altered m6A and differentially expressed mRNAs(DEmRNAs)in DC.METHODS Anterior lens capsules were collected from the control subjects and patients with DC.M6A epitranscriptomic microarray was performed to investigate the altered m6A modifications and determine the DEmRNAs.Through Gene Ontology and pathway enrichment(Kyoto Encyclopedia of Genes and Genomes)analyses,the potential role played by dysregulated m6A modification was predicted.Real-time polymerase chain reaction was further carried out to identify the dysregulated expression of RNA methyltransferases,demethylases,and readers.RESULTS Increased m6A abundance levels were found in the total mRNA of DC samples.Bioinformatics analysis predicted that ferroptosis pathways could be associated with m6A-modified mRNAs.The levels of five methylation-related genes-RBM15,WTAP,ALKBH5,FTO,and YTHDF1-were upregulated in DC samples.Upregulation of RBM15 expression was verified in SRA01/04 cells with high-glucose medium and in samples from DC patients.CONCLUSION M6a mRNA modifications may be involved in DC progression via the ferroptosis pathway,rendering novel insights into therapeutic strategies for DC.展开更多
The biological roles of N6 methylation of nucleic acids have been extensively studied.Adenine methylation of RNA is the most prevalent RNA modification and has widespread effects on RNA splicing,translation,localizati...The biological roles of N6 methylation of nucleic acids have been extensively studied.Adenine methylation of RNA is the most prevalent RNA modification and has widespread effects on RNA splicing,translation,localization,and stability.Aberrant dynamic regulation of RNA N6-methyladenosine(m6 A)has been reported in numerous human diseases,including several cancers.In recent years,eukaryotic DNA N6-methyladenosine(6 mA)has also been reported and implicated in cancer progression and tumorigenesis.In this review,we summarize the contributions of N6-methyladenosine modification to cancer biology and pathogenesis in the context of both RNA and DNA.We also highlight the clinical relevance of targeting these modifications as a therapeutic strategy for cancer.展开更多
BACKGROUND Severe acute pancreatitis(SAP)is a deadly inflammatory disease with complex pathogenesis and lack of effective therapeutic options.N6-methyladenosine(m6A)modification of circRNAs plays important roles in ph...BACKGROUND Severe acute pancreatitis(SAP)is a deadly inflammatory disease with complex pathogenesis and lack of effective therapeutic options.N6-methyladenosine(m6A)modification of circRNAs plays important roles in physiological and pathological processes.However,the roles of m6A circRNA in the pathological process of SAP remains unknown.AIM To identify transcriptome-wide map of m6A circRNAs and to determine their biological significance and potential mechanisms in SAP.METHODS The SAP in C57BL/6 mice was induced using 4%sodium taurocholate salt.The transcriptome-wide map of m6A circRNAs was identified by m6A-modified RNA immunoprecipitation sequencing.The biological significance of circRNAs with differentially expressed m6A peaks was evaluated through gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis.The underlying mechanism of m6A circRNAs in SAP was analyzed by constructing of m6A circRNAmicroRNA networks.The expression of demethylases was determined by quantitative polymerase chain reaction and western blot to deduce the possible mechanism of reversible m6A process in SAP.RESULTS Fifty-seven circRNAs with differentially expressed m6A peaks were identified by m6A-modified RNA immunoprecipitation sequencing,of which 32 were upregulated and 25 downregulated.Functional analysis of these m6A circRNAs in SAP found some important pathways involved in the pathogenesis of SAP,such as regulation of autophagy and protein digestion.In m6A circRNA–miRNA networks,several important miRNAs participated in the occurrence and progression of SAP were found to bind to these m6A circRNAs,such as miR-24-3p,miR-26a,miR-92b,miR-216b,miR-324-5p and miR-762.Notably,the total m6A level of circRNAs was reduced,while the demethylase alkylation repair homolog 5 was upregulated in SAP.CONCLUSION m6A modification of circRNAs may be involved in the pathogenesis of SAP.Our findings may provide novel insights to explore the possible pathogenetic mechanism of SAP and seek new potential therapeutic targets for SAP.展开更多
BACKGROUND Increasing evidence has demonstrated that N6-methyladenosine(m6A)RNA modification plays an essential role in a wide range of pathological conditions.Impaired autophagy is a critical hallmark of acute pancre...BACKGROUND Increasing evidence has demonstrated that N6-methyladenosine(m6A)RNA modification plays an essential role in a wide range of pathological conditions.Impaired autophagy is a critical hallmark of acute pancreatitis(AP).AIM To explore the role of the m6A modification of ZKSCAN3 in the regulation of autophagy in AP.METHODS The AP mouse cell model was established by cerulein-treated mouse pancreatic acinar cells(MPC-83),and the results were confirmed by the levels of amylase and inflammatory factors.Autophagy activity was evaluated by specific identification of the autophagy-related microstructure and the expression of autophagy-related genes.ZKSCAN3 and ALKBH5 were knocked down to study the function in AP.A m6A RNA binding protein immunoprecipitation assay was used to study how the m6A modification of ZKSCAN3 mRNA is regulated by ALKBH.RESULTS The increased expression of amylase and inflammatory factors in the supernatant and the accumulation of autophagic vacuoles verified that the AP mouse cell model was established.The downregulation of LAMP2 and upregulation of LC3-II/I and SQSTM1 demonstrated that autophagy was impaired in AP.The expression of ZKSCAN3 was upregulated in AP.Inhibition of ZKSCAN3 increased the expression of LAMP2 and decreased the expression of the inflammatory factors,LC3-II/I and SQSTM1.Furthermore,ALKBH5 was upregulated in AP.Knockdown of ALKBH5 downregulated ZKSCAN3 expression and restored decreased autophagic flux in AP.Notably,the bioinformatic analysis revealed 23 potential m6A modification sites on ZKSCAN3 mRNA.The m6A modification of ZKSCAN3 mRNA was significantly decreased in AP.Knockdown of ALKBH5 increased the modification of ZKSCAN3 mRNA,which confirmed that ALKBH5 upregulated ZKSCAN3 expression in a m6A-dependent manner.CONCLUSION ALKBH5 inhibits autophagic flux through m6A demethylation of ZKSCAN3 mRNA in AP,thereby aggravating the severity of the disease.展开更多
Background:The mechanism of metabolism reprogramming is an unsolved problem in clear cell renal cell carcinoma(ccRCC).Recently,it was discovered that the Hippo pathway altered tumor metabolism and promoted tumor progr...Background:The mechanism of metabolism reprogramming is an unsolved problem in clear cell renal cell carcinoma(ccRCC).Recently,it was discovered that the Hippo pathway altered tumor metabolism and promoted tumor progression.Thus,this study aimed at identifying key regulators of metabolism reprogramming and the Hippo pathway in ccRCC and pinpointing potential therapeutic targets for ccRCC patients.Methods:Hippo-related gene sets and metabolic gene sets were used to screen potential regulators of the Hippo pathway in ccRCC.Public databases and samples from patients were applied to investigate the association of dihydrolipoamide branched chain transacylase E2(DBT)with ccRCC and Hippo signaling.The role of DBT was confirmed by gain or loss of function assays in vitro and in vivo.Mechanistic results were yielded by luciferase reporter assay,immunoprecipitation,mass spectroscopy,and mutational studies.Results:DBT was confirmed as a Hippo-related marker with significant prognostic predictive value,and its downregulationwas caused bymethyltransferaselike-3(METTL3)-mediated N6-methyladenosine(m6A)modification in ccRCC.Functional studies specified DBT as a tumor suppressor for inhibiting tumor progression and correcting the lipid metabolism disorder in ccRCC.Mechanistic findings revealed that annexin A2(ANXA2)interacted with the lipoyl-binding domain of DBT to activate Hippo signaling which led to decreased nuclear localization of yes1-associated transcriptional regulator(YAP)and transcriptional repression of lipogenic genes.Conclusions:This study demonstrated a tumor-suppressive role for the DBT/ANXA2/YAP axis-regulated Hippo signaling and suggested DBT as a potential target for pharmaceutical intervention in ccRCC.展开更多
Background:N6-methyladenosine(m^(6)A)modification is the most common modification that occurs in eukaryotes.Although substantial effort has been made in the prevention and treatment of gastric cancer(GC)in recent year...Background:N6-methyladenosine(m^(6)A)modification is the most common modification that occurs in eukaryotes.Although substantial effort has been made in the prevention and treatment of gastric cancer(GC)in recent years,the prognosis of GC patients remains unsatisfactory.The regulatory mechanism between m^(6)A modification and GC development needs to be elucidated.In this study,we examined m^(6)A modification and the downstream mechanism in GC.Methods:Dot blotting assays,The Cancer Genome Atlas analysis,and quantitative real‑time PCR(qRT-PCR)were used to measure the m^(6)A levels in GC tissues.Methylated RNA-immunoprecipitation sequencing and RNA sequencingwere performed to identify the targets ofm^(6)Amodification.Western blotting,Transwell,wound healing,and angiogenesis assays were conducted to examine the role of centromere protein F(CENPF)in GC in vitro.Xenograft,immunohistochemistry,and in vivo metastasis experiments were conducted to examine the role of CENPF in GC in vivo.Methylated RNA-immunoprecipitation-qPCR,RNA immunoprecipitation-qPCR and RNA pulldown assays were used to verify the m^(6)A modification sites of CENPF.Gain/loss-of-function and rescue experiments were conducted to determine the relationship between CENPF and the mitogen-activated protein kinase(MAPK)signaling pathway in GC cells.Coimmunoprecipitation,mass spectrometry,qRT-PCR,and immunofluorescence assays were performed to explore the proteins that interact with CENPF and elucidate the regulatory mechanisms between them.Results:CENPF was upregulated in GC and facilitated the metastasis of GC both in vitro and in vivo.Mechanistically,increasedm^(6)A modification of CENPF was mediated by methyltransferase 3,and this modified molecule could be recognized by heterogeneous nuclear ribonucleoprotein A2/B1(HNRNPA2B1),thereby promoting its mRNA stability.In addition,the metastatic phenotype of CENPF was dependent on the MAPK signaling pathway.Furthermore,CENPF could bind to FAK and promote its localization in the cytoplasm.Moreover,we discovered that high expression of CENPF was related to lymphatic invasion and overall survival in GC patients.Conclusions:Our findings revealed that increased m^(6)A modification of CENPF facilitates the metastasis and angiogenesis of GC through the CENPF/FAK/MAPK and epithelial-mesenchymal transition axis.CENPF expression was correlated with the clinical features of GC patients;therefore,CENPF may serve as a prognostic marker of GC.展开更多
Accumulating evidence indicates that RNA methylation at N6-methyladenosine(m6A)plays an important regulatory role in gene expression and aberrant mRNA m6A modification is often associated with a variety of cancers.How...Accumulating evidence indicates that RNA methylation at N6-methyladenosine(m6A)plays an important regulatory role in gene expression and aberrant mRNA m6A modification is often associated with a variety of cancers.However,little is known whether and how m6A-modification impacts long non-coding RNA(lncRNA)and lncRNA-mediated tumorigenesis,particularly in pancreatic ductal adenocarcinoma(PDAC).In the present study,we report that a previously uncharacterized lncRNA,LINC00901,promotes pancreatic cancer cell growth and invasion and moreover,LINC00901 is subject to m6A modification which regulates its expression.In this regard,YTHDF1 serves as a reader for the m6A modified LINC00901 and downregulates the LINC00901 level.Notably,two conserved m6A sites in LINC00901 are critical to the recognition of LINC00901 by YTHDF1.Finally,RNA sequencing(RNA-seq)and gene function analysis revealed that LINC00901 positively regulates MYC through upregulation of IGF2BP2,a known RNA binding protein that can enhance MYC mRNA stability.Together,our results suggest that there is a LINC00901-IGF2BP2-MYC axis through which LINC00901 promotes PDAC progression in an m6A dependent manner.展开更多
Increasing evidence indicates that mRNAs are often subject to posttranscriptional modifications.Among them,N6-methyladenosine(m6A),which has been shown to play key roles in RNA splicing,stability,nuclear export,and tr...Increasing evidence indicates that mRNAs are often subject to posttranscriptional modifications.Among them,N6-methyladenosine(m6A),which has been shown to play key roles in RNA splicing,stability,nuclear export,and translation,is the most abundant modification of RNA.Extensive studies of m6A modification of mRNAs have been carried out,while little is known about m6A modification of long non-coding RNAs(lncRNAs).Recently,several studies reported m6A modification of lncRNAs.In this review,we focus on these m6A-modified lncRNAs and discuss possible functions of m6A modification.展开更多
N6-methyladenosine(m^(6)A)is a prevalent methylation modification and plays a vital role in various biological processes,such as metabolism,mRNA processing,synthesis,and transport.Recent studies have suggested that m^...N6-methyladenosine(m^(6)A)is a prevalent methylation modification and plays a vital role in various biological processes,such as metabolism,mRNA processing,synthesis,and transport.Recent studies have suggested that m^(6)A modification is related to common diseases such as cancer,tumours,and obesity.Therefore,accurate prediction of methylation sites in RNA sequences has emerged as a critical issue in the area of bioinformatics.However,traditional high-throughput sequencing and wet bench experimental techniques have the disadvantages of high costs,significant time requirements and inaccurate identification of sites.But through the use of traditional experimental methods,researchers have produced many large databases of m^(6)A sites.With the support of these basic databases and existing deep learning methods,we developed an m^(6)A site predictor named DeepM6ASeq-EL,which integrates an ensemble of five LSTM and CNN classifiers with the combined strategy of hard voting.Compared to the state-of-the-art prediction method WHISTLE(average AUC 0.948 and 0.880),the DeepM6ASeq-EL had a lower accuracy in m^(6)A site prediction(average AUC:0.861 for the full transcript models and 0.809 for the mature messenger RNA models)when tested on six independent datasets.展开更多
Background and Aims:Numerous studies have explored the important role of N6-methyladenosine(m^(6)A)in cancer.Nonetheless,the interaction between m^(6)A and long noncoding RNAs(lncRNAs)is poorly investigated.Herein,we ...Background and Aims:Numerous studies have explored the important role of N6-methyladenosine(m^(6)A)in cancer.Nonetheless,the interaction between m^(6)A and long noncoding RNAs(lncRNAs)is poorly investigated.Herein,we systematically analyzed the role and prognostic value of m^(6)A-related lncRNAs in hepatocellular carcinoma(HCC).Methods:The m^(6)A-related lncRNAs were identified based on the correlation coefficients with m^(6)A-related genes in HCC from The Cancer Genome Atlas.Subsequently,a novel risk score model was determined using the least absolute shrinkage and selection operator Cox regression analyses.Univariate and multivariate Cox analyses were used to identify independent prog-nostic factors for overall survival(OS)of HCC;thereafter,a prognostic nomogram was constructed.Results:A total of 259 lncRNAs showed significant correlations with m^(6)A in HCC,while 29 lncRNAs had prognostic significance.Further,six critical m^(6)A-related lncRNAs(NRAV,SNHG3,KDM4A-AS1,AC074117.1,AC025176.1,and AL031985.3)were screened out to construct a novel risk score model which classified HCC patients into high-and low-risk groups.Survival analy-ses revealed that patients in the high-risk group exhibited worse OS,both in the training and validation groups.The risk score was also identified as an independent prognostic factor of OS,and a nomogram was established and verified with superior prediction capacity.Besides,the risk score signifi-cantly correlated with the expression of immune checkpoint genes and immune subtypes.Conclusions:These findings indicated the significant role of m^(6)A-related lncRNAs in HCC and the potential application of the novel risk score model for prognostic prediction.展开更多
Ribosome RNA(rRNA)accounts for more than 80%of the cell's total RNA,while the physiological functions of rRNA modifications are poorly understood.Mutations of 18S rRNA m6A methyltransferase METTL5 cause intellectu...Ribosome RNA(rRNA)accounts for more than 80%of the cell's total RNA,while the physiological functions of rRNA modifications are poorly understood.Mutations of 18S rRNA m6A methyltransferase METTL5 cause intellectual disability,microcephaly,and facial dysmorphisms in patients,however,little is known about the underlying mechanisms.In this study,we identified METTL5 protein complex and revealed that METTL5 mainly interacts with RNA binding proteins and ribosome proteins.Functionally,we found that Mettl5 knockout in mESCs leads to the abnormal craniofacial and nervous development.Moreover,using Mettl5 knockout mouse model,we further demonstrated that Mettl5 knockout mice exhibit intellectual disability,recapitulating the human phenotype.Mechanistically,we found that Mettl5 maintains brain function and intelligence by regulating the myelination process.Our study uncovered the causal correlation between mis-regulated 18S rRNA m6A modification and neural function defects,supporting the important physiological functions of rRNA modifications in human diseases.展开更多
Objective:Histone modification has a significant effect on gene expression.Enhancer of zeste homolog 2(EZH2)contributes to the epigenetic silencing of target chromatin through its roles as a histone-lysine N-methyltra...Objective:Histone modification has a significant effect on gene expression.Enhancer of zeste homolog 2(EZH2)contributes to the epigenetic silencing of target chromatin through its roles as a histone-lysine N-methyltransferase enzyme.The development of anoikis resistance in tumor cells is considered to be a critical step in the metastatic process of primary malignant tumors.The purpose of this study was to investigate the effect and mechanism of anoikis resistance in ovarian adenocarcinoma peritoneal metastasis.Methods:In addition to examining EZH2 protein expression in ovarian cancer omental metastatic tissues,we established a model of ovarian cancer cell anoikis and a xenograft tumor model in nude mice.Anoikis resistance and ovarian cancer progression were tested after EZH2 and N6-methyladenosine(m6A)levels were modified.Results:EZH2 expression was significantly higher in ovarian cancer omental metastatic tissues than in normal ovarian tissues.Reducing the level of EZH2 decreased the level of m6A and ovarian cancer cell anoikis resistance in vitro and inhibited ovarian cancer progression in vivo.M6a regulation altered the effect of EZH2 on anoikis resistance.Conclusion:Our results indicate that EZH2 contributes to anoikis resistance and promotes ovarian adenocarcinoma abdominal metastasis by m6A modification.Our findings imply the potential of the clinical application of m6A and EZH2 for patients with ovarian cancer.展开更多
Background: N6-Methyladenosine(m^6A), the most prevalent modification in mammalian m RNA, plays important roles in numerous biological processes. Several m^6A associated proteins such as methyltransferase like 3(METTL...Background: N6-Methyladenosine(m^6A), the most prevalent modification in mammalian m RNA, plays important roles in numerous biological processes. Several m^6A associated proteins such as methyltransferase like 3(METTL3),methyltransferase like 14(METTL14), α-ketoglutarate-dependent dioxygenase Alk B homolog 5(ALKBH5) and YTH domain containing 2(YTHDC2) are involved in the regulation of spermatogenesis and oogenesis. However, the role of the first detected m^6A demethylase, fat mass and obesity associate protein(FTO), in germ cells remains elusive.Elucidation of FTO roles in the regulation of germ cell fate will provide novel insights into the mammalian reproduction.Methods: Mouse GC-1 spg cells were treated with the ester form of meclofenamic acid(MA2) to inhibit the demethylase activity of FTO. The cellular m^6A and m^6Amlevel were analyzed through high performance liquid chromatography combined with tandem mass spectrometry(HPLC/MS-MS). The cell apoptosis was detected via TUNEL and flow cytometry. The cell proliferation was detected through Ed U and western blot. The m RNA level of core cyclin dependent kinases(CDKs) was quantified via q-PCR. RNA decay assay were performed to detect RNA stability. Dual fluorescence assay was conducted to study whether MA2 affects the expression of CDK2 dependent on the m^6A modification at 3’UTR.Results: MA2 significantly increased the cellular m^6A level and down-regulated the expression of CDK1, CDK2, CDK6 and Cd C25 a, resulting in arrest of G1/S transition and decrease of cell proliferation. MA2 downregulated CDK2 m RNA stability. Additionally, mutation of the predicted m^6A sites in the Cdk2–3’UTR could mitigated the degradation of CDK2 m RNA after MA2 treatment.Conclusion: MA2 affected CDKs expression through the m^6A-dependent m RNA degradation pathway, and thus repressed spermatogonial proliferation.展开更多
The unicellular green alga Chlamydomonas reinhardtii(hereafter Chlamydomonas)possesses both plant and animal attributes,and it is an ideal model organism for studying fundamental processes such as photosynthesis,sexua...The unicellular green alga Chlamydomonas reinhardtii(hereafter Chlamydomonas)possesses both plant and animal attributes,and it is an ideal model organism for studying fundamental processes such as photosynthesis,sexual reproduction,and life cycle.N^(6)-methyladenosine(m^(6)A)is the most prevalent mRNA modification,and it plays important roles during sexual reproduction in animals and plants.However,the pattern and function of m^(6)A modification during the sexual reproduction of Chlamydomonas remain unknown.Here,we performed transcriptome and methylated RNA immunoprecipitation sequencing(MeRIP-seq)analyses on six samples from different stages during sexual reproduction of the Chlamydomonas life cycle.The results show that m^(6)A modification frequently occurs at the main motif of DRAC(D=G/A/U,R=A/G)in Chlamydomonas mRNAs.Moreover,m^(6)A peaks in Chlamydomonas mRNAs are mainly enriched in the 30 untranslated regions(30 UTRs)and negatively correlated with the abundance of transcripts at each stage.In particular,there is a significant negative correlation between the expression levels and the m^(6)A levels of genes involved in the microtubule-associated pathway,indicating that m^(6)A modification influences the sexual reproduction and the life cycle of Chlamydomonas by regulating microtubule-based movement.In summary,our findings are the first to demonstrate the distribution and the functions of m^(6)A modification in Chlamydomonas mRNAs and provide new evolutionary insights into m^(6)A modification in the process of sexual reproduction in other plant organisms.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
Objective:Epigenetic aberration plays an important role in the development and progression of hepatocellular carcinoma(HCC).However,the alteration of RNA N6-methyladenosine(m6A)modifications and its role in HCC progre...Objective:Epigenetic aberration plays an important role in the development and progression of hepatocellular carcinoma(HCC).However,the alteration of RNA N6-methyladenosine(m6A)modifications and its role in HCC progression remain unclear.We therefore aimed to provide evidence using bioinformatics analysis.Methods:We comprehensively analyzed the m6A regulator modification patterns of 605 HCC samples and correlated them with metabolic alteration characteristics.We elucidated 390 gene-based m6A-related signatures and defined an m6Ascore to quantify m6A modifications.We then assessed their values for predicting prognoses and therapeutic responses in HCC patients.Results:We identified 3 distinct m6A modification patterns in HCC,and each pattern had distinct metabolic characteristics.The evaluation of m6A modification patterns using m6Ascores could predict the prognoses,tumor stages,and responses to sorafenib treatments of HCC patients.A nomogram based on m6Ascores showed high accuracy in predicting the overall survival of patients.The area under the receiver operating characteristic curve of predictions of 1,3,and 5-year overall survivals were 0.71,0.69,and 0.70 in the training cohort,and in the test cohort it was 0.74,0.75,and 0.71,respectively.M6Acluster C1,which corresponded to hypoactive mRNA methylation,lower expression of m6A regulators,and a lower m6Ascore,was characterized by metabolic hyperactivity,lower tumor stage,better prognosis,and lower response to sorafenib treatment.In contrast,m6Acluster C3 was distinct in its hyperactive mRNA methylations,higher expression of m6A regulators,and higher m6Ascores,and was characterized by hypoactive metabolism,advanced tumor stage,poorer prognosis,and a better response to sorafenib.The m6Acluster,C2,was intermediate between C1 and C3.Conclusions:HCCs harbored distinct m6A regulator modification patterns that contributed to the metabolic heterogeneity and diversity of HCC.Development of m6A gene signatures and the m6Ascore provides a more comprehensive understanding of m6A modifications in HCC,and helps predict the prognosis and treatment response.展开更多
基金Key Project Research and Development Plan of Hainan Province(No.ZDYF2020134,ZDYF2022SHFZ283)Natural Science Foundation of Hainan Province(No.821QN391)。
文摘N6-methyladenosine(m6A)is a reversible epigenetic modification, which is one of the most abundant modifiers in eukaryotic cells and has been commonly reported in messenger RNAs and non-coding RNAs. The processing modification of m6A regulates RNA transcription, processing, splicing, degradation, and translation, and plays an important role in the biological process of tumors. Circular RNA, which lacks the 5' cap structure, has been mistakenly regarded as a "junk sequence" generated by accidental shearing during the transcription process. However, it has been found that circRNAs can be involved in tumor invasion and metastasis through microRNAs, binding proteins, translated peptides, and m6A modifications. In this paper, we reviewed the role of m6A modifications in circRNA regulation and their functions in hepatocellular carcinoma and discussed their potential clinical applications and future development in this field.
基金supported by funds from the National Natural Science Foundation of China (Grant No.U21A20249)China Postdoctoral Science Foundation (2022 M712794)。
文摘Background Intramuscular fat(IMF)content is a critical indicator of pork quality,and abnormal IMF is also relevant to human disease as well as aging.Although N6-methyladenosine(m^(6)A)RNA modification was recently found to regulate adipogenesis in porcine intramuscular fat,however,the underlying molecular mechanisms was still unclear.Results In this work,we collected 20 longissimus dorsi muscle samples with high(average 3.95%)or low IMF content(average 1.22%)from a unique heterogenous swine population for m^(6)A sequencing(m^(6)A-seq).We discovered 70genes show both differential RNA expression and m^(6)A modification from high and low IMF group,including ADIPOQ and SFRP1,two hub genes inferred through gene co-expression analysis.Particularly,we observed ADIPOQ,which contains three m^(6)A modification sites within 3’untranslated and protein coding region,could promote porcine intramuscular preadipocyte differentiation in an m^(6)A-dependent manner.Furthermore,we found the YT521-B homology domain family protein 1(YTHDF1)could target and promote ADIPOQ mRNA translation.Conclusions Our study provided a comprehensive profiling of m^(6)A methylation in porcine longissimus dorsi muscle and characterized the involvement of m^(6)A epigenetic modification in the regulation of ADIPOQ mRNA on IMF deposition through an m^(6)A-YTHDF1-dependent manner.
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Supported by the National Natural Science Foundation of China,No.82171039.
文摘BACKGROUND Cataracts remain a prime reason for visual disturbance and blindness all over the world,despite the capacity for successful surgical replacement with artificial lenses.Diabetic cataract(DC),a metabolic complication,usually occurs at an earlier age and progresses faster than age-related cataracts.Evidence has linked N6-methyladenosine(m6A)to DC progression.However,there exists a lack of understanding regarding RNA m6A modifications and the role of m6A in DC pathogenesis.AIM To elucidate the role played by altered m6A and differentially expressed mRNAs(DEmRNAs)in DC.METHODS Anterior lens capsules were collected from the control subjects and patients with DC.M6A epitranscriptomic microarray was performed to investigate the altered m6A modifications and determine the DEmRNAs.Through Gene Ontology and pathway enrichment(Kyoto Encyclopedia of Genes and Genomes)analyses,the potential role played by dysregulated m6A modification was predicted.Real-time polymerase chain reaction was further carried out to identify the dysregulated expression of RNA methyltransferases,demethylases,and readers.RESULTS Increased m6A abundance levels were found in the total mRNA of DC samples.Bioinformatics analysis predicted that ferroptosis pathways could be associated with m6A-modified mRNAs.The levels of five methylation-related genes-RBM15,WTAP,ALKBH5,FTO,and YTHDF1-were upregulated in DC samples.Upregulation of RBM15 expression was verified in SRA01/04 cells with high-glucose medium and in samples from DC patients.CONCLUSION M6a mRNA modifications may be involved in DC progression via the ferroptosis pathway,rendering novel insights into therapeutic strategies for DC.
基金supported by a grant from Westlake University Startup Funding(Grant No.101476021901)。
文摘The biological roles of N6 methylation of nucleic acids have been extensively studied.Adenine methylation of RNA is the most prevalent RNA modification and has widespread effects on RNA splicing,translation,localization,and stability.Aberrant dynamic regulation of RNA N6-methyladenosine(m6 A)has been reported in numerous human diseases,including several cancers.In recent years,eukaryotic DNA N6-methyladenosine(6 mA)has also been reported and implicated in cancer progression and tumorigenesis.In this review,we summarize the contributions of N6-methyladenosine modification to cancer biology and pathogenesis in the context of both RNA and DNA.We also highlight the clinical relevance of targeting these modifications as a therapeutic strategy for cancer.
基金the National Natural Science Foundation of China,No.81772001the National Clinical Key Subject of China,No.41732113.
文摘BACKGROUND Severe acute pancreatitis(SAP)is a deadly inflammatory disease with complex pathogenesis and lack of effective therapeutic options.N6-methyladenosine(m6A)modification of circRNAs plays important roles in physiological and pathological processes.However,the roles of m6A circRNA in the pathological process of SAP remains unknown.AIM To identify transcriptome-wide map of m6A circRNAs and to determine their biological significance and potential mechanisms in SAP.METHODS The SAP in C57BL/6 mice was induced using 4%sodium taurocholate salt.The transcriptome-wide map of m6A circRNAs was identified by m6A-modified RNA immunoprecipitation sequencing.The biological significance of circRNAs with differentially expressed m6A peaks was evaluated through gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis.The underlying mechanism of m6A circRNAs in SAP was analyzed by constructing of m6A circRNAmicroRNA networks.The expression of demethylases was determined by quantitative polymerase chain reaction and western blot to deduce the possible mechanism of reversible m6A process in SAP.RESULTS Fifty-seven circRNAs with differentially expressed m6A peaks were identified by m6A-modified RNA immunoprecipitation sequencing,of which 32 were upregulated and 25 downregulated.Functional analysis of these m6A circRNAs in SAP found some important pathways involved in the pathogenesis of SAP,such as regulation of autophagy and protein digestion.In m6A circRNA–miRNA networks,several important miRNAs participated in the occurrence and progression of SAP were found to bind to these m6A circRNAs,such as miR-24-3p,miR-26a,miR-92b,miR-216b,miR-324-5p and miR-762.Notably,the total m6A level of circRNAs was reduced,while the demethylase alkylation repair homolog 5 was upregulated in SAP.CONCLUSION m6A modification of circRNAs may be involved in the pathogenesis of SAP.Our findings may provide novel insights to explore the possible pathogenetic mechanism of SAP and seek new potential therapeutic targets for SAP.
基金Supported by National Natural Science Foundation of China,No.81802450and Natural Science Foundation of Hunan Province,No.2020JJ4133 and No.2021JJ31135.
文摘BACKGROUND Increasing evidence has demonstrated that N6-methyladenosine(m6A)RNA modification plays an essential role in a wide range of pathological conditions.Impaired autophagy is a critical hallmark of acute pancreatitis(AP).AIM To explore the role of the m6A modification of ZKSCAN3 in the regulation of autophagy in AP.METHODS The AP mouse cell model was established by cerulein-treated mouse pancreatic acinar cells(MPC-83),and the results were confirmed by the levels of amylase and inflammatory factors.Autophagy activity was evaluated by specific identification of the autophagy-related microstructure and the expression of autophagy-related genes.ZKSCAN3 and ALKBH5 were knocked down to study the function in AP.A m6A RNA binding protein immunoprecipitation assay was used to study how the m6A modification of ZKSCAN3 mRNA is regulated by ALKBH.RESULTS The increased expression of amylase and inflammatory factors in the supernatant and the accumulation of autophagic vacuoles verified that the AP mouse cell model was established.The downregulation of LAMP2 and upregulation of LC3-II/I and SQSTM1 demonstrated that autophagy was impaired in AP.The expression of ZKSCAN3 was upregulated in AP.Inhibition of ZKSCAN3 increased the expression of LAMP2 and decreased the expression of the inflammatory factors,LC3-II/I and SQSTM1.Furthermore,ALKBH5 was upregulated in AP.Knockdown of ALKBH5 downregulated ZKSCAN3 expression and restored decreased autophagic flux in AP.Notably,the bioinformatic analysis revealed 23 potential m6A modification sites on ZKSCAN3 mRNA.The m6A modification of ZKSCAN3 mRNA was significantly decreased in AP.Knockdown of ALKBH5 increased the modification of ZKSCAN3 mRNA,which confirmed that ALKBH5 upregulated ZKSCAN3 expression in a m6A-dependent manner.CONCLUSION ALKBH5 inhibits autophagic flux through m6A demethylation of ZKSCAN3 mRNA in AP,thereby aggravating the severity of the disease.
基金National Natural Science Foundation of China,Grant/Award Numbers:81874090,82202911National Key Scientific Instrument and Equipment Development Project,Grant/Award Number:81927807。
文摘Background:The mechanism of metabolism reprogramming is an unsolved problem in clear cell renal cell carcinoma(ccRCC).Recently,it was discovered that the Hippo pathway altered tumor metabolism and promoted tumor progression.Thus,this study aimed at identifying key regulators of metabolism reprogramming and the Hippo pathway in ccRCC and pinpointing potential therapeutic targets for ccRCC patients.Methods:Hippo-related gene sets and metabolic gene sets were used to screen potential regulators of the Hippo pathway in ccRCC.Public databases and samples from patients were applied to investigate the association of dihydrolipoamide branched chain transacylase E2(DBT)with ccRCC and Hippo signaling.The role of DBT was confirmed by gain or loss of function assays in vitro and in vivo.Mechanistic results were yielded by luciferase reporter assay,immunoprecipitation,mass spectroscopy,and mutational studies.Results:DBT was confirmed as a Hippo-related marker with significant prognostic predictive value,and its downregulationwas caused bymethyltransferaselike-3(METTL3)-mediated N6-methyladenosine(m6A)modification in ccRCC.Functional studies specified DBT as a tumor suppressor for inhibiting tumor progression and correcting the lipid metabolism disorder in ccRCC.Mechanistic findings revealed that annexin A2(ANXA2)interacted with the lipoyl-binding domain of DBT to activate Hippo signaling which led to decreased nuclear localization of yes1-associated transcriptional regulator(YAP)and transcriptional repression of lipogenic genes.Conclusions:This study demonstrated a tumor-suppressive role for the DBT/ANXA2/YAP axis-regulated Hippo signaling and suggested DBT as a potential target for pharmaceutical intervention in ccRCC.
基金Special Foundation for National Science and Technology Basic Research Program of China,Grant/Award Number:2019FY101104National Natural Science Foundation of China,Grant/Award Numbers:81871946,82072708+6 种基金Primary Research&Development Plan of Jiangsu Province,Grant/Award Number:BE2016786Program for Development of Innovative Research Team in the First Affiliated Hospital of NJMUPriority Academic Program Development of Jiangsu Higher Education Institutions,Grant/Award Number:JX10231801Jiangsu Key Medical Discipline,Grant/Award Number:ZDXKA2016005Jiangsu Key Lab of Cancer Biomarkers,Prevention and TreatmentCollaborative Innovation Centre for Cancer Personalized MedicineNanjing Medical University。
文摘Background:N6-methyladenosine(m^(6)A)modification is the most common modification that occurs in eukaryotes.Although substantial effort has been made in the prevention and treatment of gastric cancer(GC)in recent years,the prognosis of GC patients remains unsatisfactory.The regulatory mechanism between m^(6)A modification and GC development needs to be elucidated.In this study,we examined m^(6)A modification and the downstream mechanism in GC.Methods:Dot blotting assays,The Cancer Genome Atlas analysis,and quantitative real‑time PCR(qRT-PCR)were used to measure the m^(6)A levels in GC tissues.Methylated RNA-immunoprecipitation sequencing and RNA sequencingwere performed to identify the targets ofm^(6)Amodification.Western blotting,Transwell,wound healing,and angiogenesis assays were conducted to examine the role of centromere protein F(CENPF)in GC in vitro.Xenograft,immunohistochemistry,and in vivo metastasis experiments were conducted to examine the role of CENPF in GC in vivo.Methylated RNA-immunoprecipitation-qPCR,RNA immunoprecipitation-qPCR and RNA pulldown assays were used to verify the m^(6)A modification sites of CENPF.Gain/loss-of-function and rescue experiments were conducted to determine the relationship between CENPF and the mitogen-activated protein kinase(MAPK)signaling pathway in GC cells.Coimmunoprecipitation,mass spectrometry,qRT-PCR,and immunofluorescence assays were performed to explore the proteins that interact with CENPF and elucidate the regulatory mechanisms between them.Results:CENPF was upregulated in GC and facilitated the metastasis of GC both in vitro and in vivo.Mechanistically,increasedm^(6)A modification of CENPF was mediated by methyltransferase 3,and this modified molecule could be recognized by heterogeneous nuclear ribonucleoprotein A2/B1(HNRNPA2B1),thereby promoting its mRNA stability.In addition,the metastatic phenotype of CENPF was dependent on the MAPK signaling pathway.Furthermore,CENPF could bind to FAK and promote its localization in the cytoplasm.Moreover,we discovered that high expression of CENPF was related to lymphatic invasion and overall survival in GC patients.Conclusions:Our findings revealed that increased m^(6)A modification of CENPF facilitates the metastasis and angiogenesis of GC through the CENPF/FAK/MAPK and epithelial-mesenchymal transition axis.CENPF expression was correlated with the clinical features of GC patients;therefore,CENPF may serve as a prognostic marker of GC.
基金supported by grants from National Natural Science Foundation of China(No.82072703 to WP,No.81772575 and No.81972455 to LY)US Department of Defense(No.CA170314 to YM).
文摘Accumulating evidence indicates that RNA methylation at N6-methyladenosine(m6A)plays an important regulatory role in gene expression and aberrant mRNA m6A modification is often associated with a variety of cancers.However,little is known whether and how m6A-modification impacts long non-coding RNA(lncRNA)and lncRNA-mediated tumorigenesis,particularly in pancreatic ductal adenocarcinoma(PDAC).In the present study,we report that a previously uncharacterized lncRNA,LINC00901,promotes pancreatic cancer cell growth and invasion and moreover,LINC00901 is subject to m6A modification which regulates its expression.In this regard,YTHDF1 serves as a reader for the m6A modified LINC00901 and downregulates the LINC00901 level.Notably,two conserved m6A sites in LINC00901 are critical to the recognition of LINC00901 by YTHDF1.Finally,RNA sequencing(RNA-seq)and gene function analysis revealed that LINC00901 positively regulates MYC through upregulation of IGF2BP2,a known RNA binding protein that can enhance MYC mRNA stability.Together,our results suggest that there is a LINC00901-IGF2BP2-MYC axis through which LINC00901 promotes PDAC progression in an m6A dependent manner.
基金This work was supported by the Natural Science Foundation of China(81773165)Hunan Province Science Fund for Distinguished Young Scholars(2018JJ1021)+1 种基金the Key R&D Program of Hunan Province(2017SK2172)the Science and Technology Foundation of Chenzhou(jsyf2017023).
文摘Increasing evidence indicates that mRNAs are often subject to posttranscriptional modifications.Among them,N6-methyladenosine(m6A),which has been shown to play key roles in RNA splicing,stability,nuclear export,and translation,is the most abundant modification of RNA.Extensive studies of m6A modification of mRNAs have been carried out,while little is known about m6A modification of long non-coding RNAs(lncRNAs).Recently,several studies reported m6A modification of lncRNAs.In this review,we focus on these m6A-modified lncRNAs and discuss possible functions of m6A modification.
基金The work was supported by the National Natural Science Foundation of China(Grant Nos.61922020,61771331,91935302).
文摘N6-methyladenosine(m^(6)A)is a prevalent methylation modification and plays a vital role in various biological processes,such as metabolism,mRNA processing,synthesis,and transport.Recent studies have suggested that m^(6)A modification is related to common diseases such as cancer,tumours,and obesity.Therefore,accurate prediction of methylation sites in RNA sequences has emerged as a critical issue in the area of bioinformatics.However,traditional high-throughput sequencing and wet bench experimental techniques have the disadvantages of high costs,significant time requirements and inaccurate identification of sites.But through the use of traditional experimental methods,researchers have produced many large databases of m^(6)A sites.With the support of these basic databases and existing deep learning methods,we developed an m^(6)A site predictor named DeepM6ASeq-EL,which integrates an ensemble of five LSTM and CNN classifiers with the combined strategy of hard voting.Compared to the state-of-the-art prediction method WHISTLE(average AUC 0.948 and 0.880),the DeepM6ASeq-EL had a lower accuracy in m^(6)A site prediction(average AUC:0.861 for the full transcript models and 0.809 for the mature messenger RNA models)when tested on six independent datasets.
基金supported in part by grants from the GuangdongGuang-dong Natural Science Foundation(Nos.2015A030313038,2015A030312013)Science and Technology Program of Guangzhou City(No.201607010024)Guangdong Key Laboratory of Liver Disease Research(No.2017B030314027).
文摘Background and Aims:Numerous studies have explored the important role of N6-methyladenosine(m^(6)A)in cancer.Nonetheless,the interaction between m^(6)A and long noncoding RNAs(lncRNAs)is poorly investigated.Herein,we systematically analyzed the role and prognostic value of m^(6)A-related lncRNAs in hepatocellular carcinoma(HCC).Methods:The m^(6)A-related lncRNAs were identified based on the correlation coefficients with m^(6)A-related genes in HCC from The Cancer Genome Atlas.Subsequently,a novel risk score model was determined using the least absolute shrinkage and selection operator Cox regression analyses.Univariate and multivariate Cox analyses were used to identify independent prog-nostic factors for overall survival(OS)of HCC;thereafter,a prognostic nomogram was constructed.Results:A total of 259 lncRNAs showed significant correlations with m^(6)A in HCC,while 29 lncRNAs had prognostic significance.Further,six critical m^(6)A-related lncRNAs(NRAV,SNHG3,KDM4A-AS1,AC074117.1,AC025176.1,and AL031985.3)were screened out to construct a novel risk score model which classified HCC patients into high-and low-risk groups.Survival analy-ses revealed that patients in the high-risk group exhibited worse OS,both in the training and validation groups.The risk score was also identified as an independent prognostic factor of OS,and a nomogram was established and verified with superior prediction capacity.Besides,the risk score signifi-cantly correlated with the expression of immune checkpoint genes and immune subtypes.Conclusions:These findings indicated the significant role of m^(6)A-related lncRNAs in HCC and the potential application of the novel risk score model for prognostic prediction.
基金This work was supported by Excellent Youth Scholars grant from National Natural Science Foundation of China(No.81922052)Distinguished Young Scholars grant from Natural Science Foundation of Guangdong(No.2019B151502011)the Guangzhou People's Livelihood Science and Technology Project(No.201903010006).
文摘Ribosome RNA(rRNA)accounts for more than 80%of the cell's total RNA,while the physiological functions of rRNA modifications are poorly understood.Mutations of 18S rRNA m6A methyltransferase METTL5 cause intellectual disability,microcephaly,and facial dysmorphisms in patients,however,little is known about the underlying mechanisms.In this study,we identified METTL5 protein complex and revealed that METTL5 mainly interacts with RNA binding proteins and ribosome proteins.Functionally,we found that Mettl5 knockout in mESCs leads to the abnormal craniofacial and nervous development.Moreover,using Mettl5 knockout mouse model,we further demonstrated that Mettl5 knockout mice exhibit intellectual disability,recapitulating the human phenotype.Mechanistically,we found that Mettl5 maintains brain function and intelligence by regulating the myelination process.Our study uncovered the causal correlation between mis-regulated 18S rRNA m6A modification and neural function defects,supporting the important physiological functions of rRNA modifications in human diseases.
基金funded by the National Natural Science Foundation of China(No.81672573)Natural Science Foundation of Xinjiang Uygur Autonomous Region(No.2021D01F21)Natural Science Foundation of Hubei Province(No.2021CFB474)。
文摘Objective:Histone modification has a significant effect on gene expression.Enhancer of zeste homolog 2(EZH2)contributes to the epigenetic silencing of target chromatin through its roles as a histone-lysine N-methyltransferase enzyme.The development of anoikis resistance in tumor cells is considered to be a critical step in the metastatic process of primary malignant tumors.The purpose of this study was to investigate the effect and mechanism of anoikis resistance in ovarian adenocarcinoma peritoneal metastasis.Methods:In addition to examining EZH2 protein expression in ovarian cancer omental metastatic tissues,we established a model of ovarian cancer cell anoikis and a xenograft tumor model in nude mice.Anoikis resistance and ovarian cancer progression were tested after EZH2 and N6-methyladenosine(m6A)levels were modified.Results:EZH2 expression was significantly higher in ovarian cancer omental metastatic tissues than in normal ovarian tissues.Reducing the level of EZH2 decreased the level of m6A and ovarian cancer cell anoikis resistance in vitro and inhibited ovarian cancer progression in vivo.M6a regulation altered the effect of EZH2 on anoikis resistance.Conclusion:Our results indicate that EZH2 contributes to anoikis resistance and promotes ovarian adenocarcinoma abdominal metastasis by m6A modification.Our findings imply the potential of the clinical application of m6A and EZH2 for patients with ovarian cancer.
基金supported in part by the National Natural Science Foundation of China(Grant No.31572401)to WZ
文摘Background: N6-Methyladenosine(m^6A), the most prevalent modification in mammalian m RNA, plays important roles in numerous biological processes. Several m^6A associated proteins such as methyltransferase like 3(METTL3),methyltransferase like 14(METTL14), α-ketoglutarate-dependent dioxygenase Alk B homolog 5(ALKBH5) and YTH domain containing 2(YTHDC2) are involved in the regulation of spermatogenesis and oogenesis. However, the role of the first detected m^6A demethylase, fat mass and obesity associate protein(FTO), in germ cells remains elusive.Elucidation of FTO roles in the regulation of germ cell fate will provide novel insights into the mammalian reproduction.Methods: Mouse GC-1 spg cells were treated with the ester form of meclofenamic acid(MA2) to inhibit the demethylase activity of FTO. The cellular m^6A and m^6Amlevel were analyzed through high performance liquid chromatography combined with tandem mass spectrometry(HPLC/MS-MS). The cell apoptosis was detected via TUNEL and flow cytometry. The cell proliferation was detected through Ed U and western blot. The m RNA level of core cyclin dependent kinases(CDKs) was quantified via q-PCR. RNA decay assay were performed to detect RNA stability. Dual fluorescence assay was conducted to study whether MA2 affects the expression of CDK2 dependent on the m^6A modification at 3’UTR.Results: MA2 significantly increased the cellular m^6A level and down-regulated the expression of CDK1, CDK2, CDK6 and Cd C25 a, resulting in arrest of G1/S transition and decrease of cell proliferation. MA2 downregulated CDK2 m RNA stability. Additionally, mutation of the predicted m^6A sites in the Cdk2–3’UTR could mitigated the degradation of CDK2 m RNA after MA2 treatment.Conclusion: MA2 affected CDKs expression through the m^6A-dependent m RNA degradation pathway, and thus repressed spermatogonial proliferation.
基金supported by the National Key R&D Program of China(Grant Nos.2019YFA0904600,2018YFA0801200,and 2021YFA0910800)the National Natural Science Foundation of China(Grant Nos.31870217 and 91940304).
文摘The unicellular green alga Chlamydomonas reinhardtii(hereafter Chlamydomonas)possesses both plant and animal attributes,and it is an ideal model organism for studying fundamental processes such as photosynthesis,sexual reproduction,and life cycle.N^(6)-methyladenosine(m^(6)A)is the most prevalent mRNA modification,and it plays important roles during sexual reproduction in animals and plants.However,the pattern and function of m^(6)A modification during the sexual reproduction of Chlamydomonas remain unknown.Here,we performed transcriptome and methylated RNA immunoprecipitation sequencing(MeRIP-seq)analyses on six samples from different stages during sexual reproduction of the Chlamydomonas life cycle.The results show that m^(6)A modification frequently occurs at the main motif of DRAC(D=G/A/U,R=A/G)in Chlamydomonas mRNAs.Moreover,m^(6)A peaks in Chlamydomonas mRNAs are mainly enriched in the 30 untranslated regions(30 UTRs)and negatively correlated with the abundance of transcripts at each stage.In particular,there is a significant negative correlation between the expression levels and the m^(6)A levels of genes involved in the microtubule-associated pathway,indicating that m^(6)A modification influences the sexual reproduction and the life cycle of Chlamydomonas by regulating microtubule-based movement.In summary,our findings are the first to demonstrate the distribution and the functions of m^(6)A modification in Chlamydomonas mRNAs and provide new evolutionary insights into m^(6)A modification in the process of sexual reproduction in other plant organisms.
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.
基金supported by the National Key Research and Development Program of China(Grant Nos.2017YFC1308604 and 2017YFC0908402)the Program of Shanghai Academic Research Leader(Grant No.20XD1400900)the National Natural Science Foundation of China(Grant Nos.81940074,81772563,and 81672820)。
文摘Objective:Epigenetic aberration plays an important role in the development and progression of hepatocellular carcinoma(HCC).However,the alteration of RNA N6-methyladenosine(m6A)modifications and its role in HCC progression remain unclear.We therefore aimed to provide evidence using bioinformatics analysis.Methods:We comprehensively analyzed the m6A regulator modification patterns of 605 HCC samples and correlated them with metabolic alteration characteristics.We elucidated 390 gene-based m6A-related signatures and defined an m6Ascore to quantify m6A modifications.We then assessed their values for predicting prognoses and therapeutic responses in HCC patients.Results:We identified 3 distinct m6A modification patterns in HCC,and each pattern had distinct metabolic characteristics.The evaluation of m6A modification patterns using m6Ascores could predict the prognoses,tumor stages,and responses to sorafenib treatments of HCC patients.A nomogram based on m6Ascores showed high accuracy in predicting the overall survival of patients.The area under the receiver operating characteristic curve of predictions of 1,3,and 5-year overall survivals were 0.71,0.69,and 0.70 in the training cohort,and in the test cohort it was 0.74,0.75,and 0.71,respectively.M6Acluster C1,which corresponded to hypoactive mRNA methylation,lower expression of m6A regulators,and a lower m6Ascore,was characterized by metabolic hyperactivity,lower tumor stage,better prognosis,and lower response to sorafenib treatment.In contrast,m6Acluster C3 was distinct in its hyperactive mRNA methylations,higher expression of m6A regulators,and higher m6Ascores,and was characterized by hypoactive metabolism,advanced tumor stage,poorer prognosis,and a better response to sorafenib.The m6Acluster,C2,was intermediate between C1 and C3.Conclusions:HCCs harbored distinct m6A regulator modification patterns that contributed to the metabolic heterogeneity and diversity of HCC.Development of m6A gene signatures and the m6Ascore provides a more comprehensive understanding of m6A modifications in HCC,and helps predict the prognosis and treatment response.
