Toxoplasma gondii is an important zoonotic parasite which has over 200 genotypes worldwide.N^(6)-methyladenosine(m^(6)A)methylation is a common epigenetic modification in messenger RNAs(mRNAs),and has been implicated ...Toxoplasma gondii is an important zoonotic parasite which has over 200 genotypes worldwide.N^(6)-methyladenosine(m^(6)A)methylation is a common epigenetic modification in messenger RNAs(mRNAs),and has been implicated in many aspects of mRNA biology.However,little is known about the difference in m^(6)A methylation among different genotypes of T.gondii.In the present study,we employed methylated RNA immunoprecipitation sequencing(MeRIP-seq)technology to identify key genes exhibiting m^(6)A methylation in the three major clonal lineages(Types I,II and III)of T.gondii tachyzoites.A total of 7,650,8,359 and 7,264 m^(6)A peaks were identified in 5,211,5,607 and 4,974 genes in tachyzoites of RH(Type I),ME49(Type II)and VEG strain(Type III),respectively.By comparing RH vs.ME49,RH vs.VEG,and ME49 vs.VEG,735,192 and 615 differentially methylated peaks(DMPs)were identified in 676,168 and 553 genes,respectively.A combined MeRIP-seq and RNA-seq analysis revealed 172,41 and 153 differentially methylated genes(DMGs)at both the m^(6)A methylation and transcriptional level.Gene Ontology term enrichment analysis of the DMPs identified differences related to Golgi apparatus,plasma membrane,signal transduction,RNA processing and catalytic step 2 spliceosome.KEGG pathway enrichment analysis showed that the DMGs are mainly involved in endocytosis,systemic lupus erythematosus and mTOR signaling pathway.These findings reveal genotype-specific differences in m^(6)A methylation,which provide new resources for further investigations of the role of m^(6)A in the pathobiology of T.gondii.展开更多
Soybean cyst nematode(SCN,Heterodera glycines)is a devastating pathogen that infects soybean(Glycine max L.Merrill)and disrupts soybean production worldwide.SCN infection upregulates or downregulates the expression of...Soybean cyst nematode(SCN,Heterodera glycines)is a devastating pathogen that infects soybean(Glycine max L.Merrill)and disrupts soybean production worldwide.SCN infection upregulates or downregulates the expression of multiple genes in soybean.However,the regulatory mechanisms that underlie these changes in gene expression remain largely unexplored.N^(6)-methyladenosine(m^(6)A)methylation,one of the most prevalent mRNA modifications,contributes to transcriptional reprogramming during plant responses to pathogen infection.Nevertheless,the role of m^(6)A methylation in establishing compatible and incompatible soybean responses to SCN has not previously been studied.Here,we performed transcriptome-wide m^(6)A profiling of soybean roots infected with virulent and avirulent populations of SCN.Compared with the compatible response,the incompatible response was associated with higher global m^(6)A methylation levels,as well as more differentially modified m^(6)A peaks(DMPs)and differentially expressed genes(DEGs).A total of 133 and 194 genes showed significant differences in both transcriptional expression and m^(6)A methylation levels in compatible and incompatible interactions;the most significantly enriched gene ontology terms associated with these genes were plant–pathogen interaction(compatible)and folate biosynthesis(incompatible).Our findings demonstrate that the m^(6)A methylation profiles of compatible and incompatible soybean responses are distinct and provide new insights into the regulatory mechanism underlying soybean response to SCN at the post-transcriptional modification level,which will be valuable for improving the SCN-resistant breeding.展开更多
RNA modifications, especially methylation of the N6 position of adenosine （A）--m6A, rep- resent an emerging research frontier in RNA biology. With the rapid development of high-throughput sequencing technology, in-d...RNA modifications, especially methylation of the N6 position of adenosine （A）--m6A, rep- resent an emerging research frontier in RNA biology. With the rapid development of high-throughput sequencing technology, in-depth study of m6A distribution and function relevance becomes feasible. However, a robust method to effectively identify m6A-modified regions has not been available yet. Here, we present a novel high-efficiency and user-friendly analysis pipeline called MeRIP-PF for the signal identification of MeRIP-Seq data in reference to controls. MeRIP-PF provides a statistical P-value for each identified m6A region based on the difference of read distribution when compared to the con- trols and also calculates false discovery rate （FDR） as a cut offto differentiate reliable m6A regions from the background. Furthermore, MeRIP-PF also achieves gene annotation ofm6A signals or peaks and produce outputs in both XLS and graphical format, which are useful for further study. MeRIP-PF is implemented in Perl and is freely available at http：//software.big.ac.cn/MeRIP-PF.html.展开更多
Evidence showed that N6-methyladenosine(m^(6)A)modification plays a pivotal role in influencing RNA fate and is strongly associated with cell growth and developmental processes in many species.However,no information r...Evidence showed that N6-methyladenosine(m^(6)A)modification plays a pivotal role in influencing RNA fate and is strongly associated with cell growth and developmental processes in many species.However,no information regarding m^(6)A modification in Eimeria tenella is currently available.In the present study,we surveyed the transcriptome-wide prevalence of m^(6)A in sporulated oocysts and unsporulated oocysts of E.tenella.Methylated RNA immunoprecipitation sequencing(MeRIP-seq)analysis showed that m^(6)A modification was most abundant in the coding sequences,followed by stop codon.There were 3,903 hypermethylated and 3,178 hypomethylated mRNAs in sporulated oocysts compared with unsporulated oocysts.Further joint analysis suggested that m^(6)A modification of the majority of genes was positively correlated with mRNA expression.The mRNA relative expression and m^(6)A level of the selected genes were confirmed by quantitative reverse transcription PCR(RT-qPCR)and MeRIP-qPCR.GO and KEGG analysis indicated that differentially m^(6)A methylated genes(DMMGs)with significant differences in mRNA expression were closely related to processes such as regulation of gene expression,epigenetic,microtubule,autophagy-other and TOR signaling.Moreover,a total of 96 DMMGs without significant differences in mRNA expression showed significant differences at protein level.GO and pathway enrichment analysis of the 96 genes showed that RNA methylation may be involved in cell biosynthesis and metabolism of E.tenella.We firstly present a map of RNA m^(6)A modification in E.tenella,which provides significant insights into developmental biology of E.tenella.展开更多
Epigenetic changes in the spinal cord play a key role in the initiation and maintenance of nerve injury-induced neuro pathic pain.N6-methyladenosine(m6A)is one of the most abundant internal RNA modifications and plays...Epigenetic changes in the spinal cord play a key role in the initiation and maintenance of nerve injury-induced neuro pathic pain.N6-methyladenosine(m6A)is one of the most abundant internal RNA modifications and plays an essential function in gene regulation in many diseases.However,the global m6A modification status of mRNA in the spinal cord at different stages after neuropathic pain is unknown.In this study,we established a neuropathic pain model in mice by preserving the complete sural nerve and only damaging the common peroneal nerve.High-throughput methylated RNA immunoprecipitation sequencing res ults showed that after spared nerve injury,there were 55 m6A methylated and diffe rentially expressed genes in the spinal cord.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway results showed that m6A modification triggered inflammatory responses and apoptotic processes in the early stages after spared nerve injury.Over time,the diffe rential gene function at postoperative day 7 was enriched in "positive regulation of neurogenesis" and "positive regulation of neural precursor cell prolife ration." These functions suggested that altered synaptic morphological plasticity was a turning point in neuropathic pain formation and maintenance.Results at postoperative day 14 suggested that the persistence of neuropathic pain might be from lipid metabolic processes,such as "very-low-density lipoprotein particle clearance," "negative regulation of choleste rol transport" and "membrane lipid catabolic process." We detected the expression of m6A enzymes and found elevated mRNA expression of Ythdf2 and Ythdf3 after spared nerve injury modeling.We speculate that m6A reader enzymes also have an important role in neuropathic pain.These results provide a global landscape of mRNA m6A modifications in the spinal cord in the spared nerve injury model at diffe rent stages after injury.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
N6-Methyladenosine(m6A)modification is a crucial post-transcriptional regulatory mechanism and the most abundant and highly conserved RNA epigenetic modification in eukaryotes.Previous studies have indicated the invol...N6-Methyladenosine(m6A)modification is a crucial post-transcriptional regulatory mechanism and the most abundant and highly conserved RNA epigenetic modification in eukaryotes.Previous studies have indicated the involvement of m6A modification in various tissue regeneration processes,including liver regeneration.Vir-like m6A methyltransferase associated protein(VIRMA)is an m6A methyltransferase with robust methylation capability.However,its role in liver regeneration remains poorly understood.In this study,we generated liver-specific Virma knockout mice using the Cre-loxP system and investigated the biological functions of VIRMA in liver regeneration using both the Associating Liver Partition and Portal vein Ligation for Staged Hepatectomy(ALPPS)mouse model and the carbon tetrachloride(CCl4)mouse model.The expression level of VIRMA was rapidly up-regulated after ALPPS surgery and gradually down-regulated during liver repair.Virma deficiency significantly impaired liver regeneration capacity and disrupted cell cycle progression.Methylated RNA immunoprecipitation sequencing(MeRIP-seq)analysis revealed that Shq1 is an effective downstream target of VIRMA-mediated m6A modification.The upregulation of Shq1 enhanced the proliferation ability of cells,which was attenuated by the specific AKT inhibitor ipatasertib.Supplementation of Shq1 in vivo alleviated the liver cell proliferation inhibition caused by Virma deficiency.Furthermore,the m6A-binding protein heterogeneous nuclear ribonucleoprotein a2b1(HNRNPA2B1)enhanced the mRNA stability of Shq1.Mechanistically,Virma deficiency resulted in decreased m6A modification on Shq1 mRNA,leading to reduced binding ability of m6A-binding protein HNRNPA2B1 with Shq1,thereby decreasing the mRNA stability of Shq1 and reducing its protein expression level.Downregulation of Shq1 inhibited the PI3K/AKT pathway,thereby suppressing cell proliferation and cell cycle progression,ultimately impeding liver regeneration.In summary,our results demonstrate that VIRMA plays a critical role in promoting liver regeneration by regulating m6A modification,providing valuable insights into the epigenetic regulation during liver regeneration.展开更多
Background： The recently emerged technology of methylated RNA immunoprecipitation sequencing （MeRIP-seq） sheds light on the study of RNA epigenetics. This new bioinformatics question calls for effective and robust ...Background： The recently emerged technology of methylated RNA immunoprecipitation sequencing （MeRIP-seq） sheds light on the study of RNA epigenetics. This new bioinformatics question calls for effective and robust peaking calling algorithms to detect mRNA methylation sites from MeRIP-seq data. Methods： We propose a Bayesian hierarchical model to detect methylation sites from MeRIP-seq data. Our modeling approach includes several important characteristics. First, it models the zero-inflated and over-dispersed counts by deploying a zero-inflated negative binomial model. Second, it incorporates a hidden Markov model （HMM） to account for the spatial dependency of neighboring read enrichment. Third, our Bayesian inference allows the proposed model to borrow strength in parameter estimation, which greatly improves the model stability when dealing with MeRIP-seq data with a small number of replicates. We use Markov chain Monte Carlo （MCMC） algorithms to simultaneously infer the model parameters in a de novo fashion. The R Shiny demo is available at https：//qiwei. shinyapps.io/BaySeqPeak and the R/C ＋＋ code is available at https：//github.com/liqiwei2000/BaySeqPeak. Results： In simulation studies, the proposed method outperformed the competing methods exomePeak and MeTPeak, especially when an excess of zeros were present in the data. In real MeRIP-seq data analysis, the proposed method identified methylation sites that were more consistent with biological knowledge, and had better spatial resolution compared to the other methods. Conclusions： In this study, we develop a Bayesian hierarchical model to identify methylation peaks in MeRIP-seq data. The proposed method has a competitive edge over existing methods in terms of accuracy, robustness and spatial resolution.展开更多
基金supported by the National Key Research and Development Program of China(2021YFC2300800,2021YFC2300802 and 2021YFC2300804)the NSFC-Yunnan Joint Fund,China(U2202201)+2 种基金the Research Fund of Shanxi Province for Introduced High-level Leading Talents,China(RFSXIHLT202101)the Special Research Fund of Shanxi Agricultural University for Highlevel Talents,China(2021XG001)the Veterinary Public Health Innovation Team of Yunnan Province,China(202105AE160014)。
文摘Toxoplasma gondii is an important zoonotic parasite which has over 200 genotypes worldwide.N^(6)-methyladenosine(m^(6)A)methylation is a common epigenetic modification in messenger RNAs(mRNAs),and has been implicated in many aspects of mRNA biology.However,little is known about the difference in m^(6)A methylation among different genotypes of T.gondii.In the present study,we employed methylated RNA immunoprecipitation sequencing(MeRIP-seq)technology to identify key genes exhibiting m^(6)A methylation in the three major clonal lineages(Types I,II and III)of T.gondii tachyzoites.A total of 7,650,8,359 and 7,264 m^(6)A peaks were identified in 5,211,5,607 and 4,974 genes in tachyzoites of RH(Type I),ME49(Type II)and VEG strain(Type III),respectively.By comparing RH vs.ME49,RH vs.VEG,and ME49 vs.VEG,735,192 and 615 differentially methylated peaks(DMPs)were identified in 676,168 and 553 genes,respectively.A combined MeRIP-seq and RNA-seq analysis revealed 172,41 and 153 differentially methylated genes(DMGs)at both the m^(6)A methylation and transcriptional level.Gene Ontology term enrichment analysis of the DMPs identified differences related to Golgi apparatus,plasma membrane,signal transduction,RNA processing and catalytic step 2 spliceosome.KEGG pathway enrichment analysis showed that the DMGs are mainly involved in endocytosis,systemic lupus erythematosus and mTOR signaling pathway.These findings reveal genotype-specific differences in m^(6)A methylation,which provide new resources for further investigations of the role of m^(6)A in the pathobiology of T.gondii.
基金supported by the National Natural Science Foundation of China(31901858 and 31901859)。
文摘Soybean cyst nematode(SCN,Heterodera glycines)is a devastating pathogen that infects soybean(Glycine max L.Merrill)and disrupts soybean production worldwide.SCN infection upregulates or downregulates the expression of multiple genes in soybean.However,the regulatory mechanisms that underlie these changes in gene expression remain largely unexplored.N^(6)-methyladenosine(m^(6)A)methylation,one of the most prevalent mRNA modifications,contributes to transcriptional reprogramming during plant responses to pathogen infection.Nevertheless,the role of m^(6)A methylation in establishing compatible and incompatible soybean responses to SCN has not previously been studied.Here,we performed transcriptome-wide m^(6)A profiling of soybean roots infected with virulent and avirulent populations of SCN.Compared with the compatible response,the incompatible response was associated with higher global m^(6)A methylation levels,as well as more differentially modified m^(6)A peaks(DMPs)and differentially expressed genes(DEGs).A total of 133 and 194 genes showed significant differences in both transcriptional expression and m^(6)A methylation levels in compatible and incompatible interactions;the most significantly enriched gene ontology terms associated with these genes were plant–pathogen interaction(compatible)and folate biosynthesis(incompatible).Our findings demonstrate that the m^(6)A methylation profiles of compatible and incompatible soybean responses are distinct and provide new insights into the regulatory mechanism underlying soybean response to SCN at the post-transcriptional modification level,which will be valuable for improving the SCN-resistant breeding.
基金supported by Grants from the Ministry of Science and Technology of China (Grant No. 2011CB944100) to JYthe Natural Science Foundation (Grant No. 30900831 and 31271372)Beijing Nova Program (Grant No. Z121105002512060)to SS
文摘RNA modifications, especially methylation of the N6 position of adenosine （A）--m6A, rep- resent an emerging research frontier in RNA biology. With the rapid development of high-throughput sequencing technology, in-depth study of m6A distribution and function relevance becomes feasible. However, a robust method to effectively identify m6A-modified regions has not been available yet. Here, we present a novel high-efficiency and user-friendly analysis pipeline called MeRIP-PF for the signal identification of MeRIP-Seq data in reference to controls. MeRIP-PF provides a statistical P-value for each identified m6A region based on the difference of read distribution when compared to the con- trols and also calculates false discovery rate （FDR） as a cut offto differentiate reliable m6A regions from the background. Furthermore, MeRIP-PF also achieves gene annotation ofm6A signals or peaks and produce outputs in both XLS and graphical format, which are useful for further study. MeRIP-PF is implemented in Perl and is freely available at http：//software.big.ac.cn/MeRIP-PF.html.
基金supported by the National Natural Science Foundation of China(31902298)the Shanxi Provincial Key Research and Development Program,China(2022ZDYF126)+2 种基金the Fund for Shanxi“1331 Project”,China(20211331-13)the Science and Technology Innovation Program of Shanxi Agricultural University,China(2017YJ10)the Special Research Fund of Shanxi Agricultural University for High-level Talents,China(2021XG001)。
文摘Evidence showed that N6-methyladenosine(m^(6)A)modification plays a pivotal role in influencing RNA fate and is strongly associated with cell growth and developmental processes in many species.However,no information regarding m^(6)A modification in Eimeria tenella is currently available.In the present study,we surveyed the transcriptome-wide prevalence of m^(6)A in sporulated oocysts and unsporulated oocysts of E.tenella.Methylated RNA immunoprecipitation sequencing(MeRIP-seq)analysis showed that m^(6)A modification was most abundant in the coding sequences,followed by stop codon.There were 3,903 hypermethylated and 3,178 hypomethylated mRNAs in sporulated oocysts compared with unsporulated oocysts.Further joint analysis suggested that m^(6)A modification of the majority of genes was positively correlated with mRNA expression.The mRNA relative expression and m^(6)A level of the selected genes were confirmed by quantitative reverse transcription PCR(RT-qPCR)and MeRIP-qPCR.GO and KEGG analysis indicated that differentially m^(6)A methylated genes(DMMGs)with significant differences in mRNA expression were closely related to processes such as regulation of gene expression,epigenetic,microtubule,autophagy-other and TOR signaling.Moreover,a total of 96 DMMGs without significant differences in mRNA expression showed significant differences at protein level.GO and pathway enrichment analysis of the 96 genes showed that RNA methylation may be involved in cell biosynthesis and metabolism of E.tenella.We firstly present a map of RNA m^(6)A modification in E.tenella,which provides significant insights into developmental biology of E.tenella.
基金National Natural Science Foundation of China,No.819 73305 (to ZQ)Science and Technology Planning Project of Guangzhou of China,No.20190401 0487 (to ZQ)+1 种基金Natural Science Foundation of Guangdong Province,China,No.2021A1515010897 (to TT)Discipline Construction Fund of Cen tral Peoples Hospital of Zhanjiang,Nos.2020A01 (to TT) and 2020A02 (to TT)。
文摘Epigenetic changes in the spinal cord play a key role in the initiation and maintenance of nerve injury-induced neuro pathic pain.N6-methyladenosine(m6A)is one of the most abundant internal RNA modifications and plays an essential function in gene regulation in many diseases.However,the global m6A modification status of mRNA in the spinal cord at different stages after neuropathic pain is unknown.In this study,we established a neuropathic pain model in mice by preserving the complete sural nerve and only damaging the common peroneal nerve.High-throughput methylated RNA immunoprecipitation sequencing res ults showed that after spared nerve injury,there were 55 m6A methylated and diffe rentially expressed genes in the spinal cord.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway results showed that m6A modification triggered inflammatory responses and apoptotic processes in the early stages after spared nerve injury.Over time,the diffe rential gene function at postoperative day 7 was enriched in "positive regulation of neurogenesis" and "positive regulation of neural precursor cell prolife ration." These functions suggested that altered synaptic morphological plasticity was a turning point in neuropathic pain formation and maintenance.Results at postoperative day 14 suggested that the persistence of neuropathic pain might be from lipid metabolic processes,such as "very-low-density lipoprotein particle clearance," "negative regulation of choleste rol transport" and "membrane lipid catabolic process." We detected the expression of m6A enzymes and found elevated mRNA expression of Ythdf2 and Ythdf3 after spared nerve injury modeling.We speculate that m6A reader enzymes also have an important role in neuropathic pain.These results provide a global landscape of mRNA m6A modifications in the spinal cord in the spared nerve injury model at diffe rent stages after injury.
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 grants from the National multidisciplinary collaborative diagnosis and treatment capacity building project for major diseases(TJZ202104,China)the Natural Science Foundation of China(82270643,82070644,82170621 and 82370645)+3 种基金the Science and Technology Major Program of Sichuan Province(2022ZDZX0019,China)1.3.5 project for disciplines of excellence,West China Hospital,Sichuan University,China(ZYJC18008,ZYGD22006)Luzhou Municipal People's Government-Southwest Medical University Science and Technology Strategic Cooperation Project,China(2024LZXNYDJ045)the Medical Science and Technology Development Project of Southwest Medical University,China(24297).
文摘N6-Methyladenosine(m6A)modification is a crucial post-transcriptional regulatory mechanism and the most abundant and highly conserved RNA epigenetic modification in eukaryotes.Previous studies have indicated the involvement of m6A modification in various tissue regeneration processes,including liver regeneration.Vir-like m6A methyltransferase associated protein(VIRMA)is an m6A methyltransferase with robust methylation capability.However,its role in liver regeneration remains poorly understood.In this study,we generated liver-specific Virma knockout mice using the Cre-loxP system and investigated the biological functions of VIRMA in liver regeneration using both the Associating Liver Partition and Portal vein Ligation for Staged Hepatectomy(ALPPS)mouse model and the carbon tetrachloride(CCl4)mouse model.The expression level of VIRMA was rapidly up-regulated after ALPPS surgery and gradually down-regulated during liver repair.Virma deficiency significantly impaired liver regeneration capacity and disrupted cell cycle progression.Methylated RNA immunoprecipitation sequencing(MeRIP-seq)analysis revealed that Shq1 is an effective downstream target of VIRMA-mediated m6A modification.The upregulation of Shq1 enhanced the proliferation ability of cells,which was attenuated by the specific AKT inhibitor ipatasertib.Supplementation of Shq1 in vivo alleviated the liver cell proliferation inhibition caused by Virma deficiency.Furthermore,the m6A-binding protein heterogeneous nuclear ribonucleoprotein a2b1(HNRNPA2B1)enhanced the mRNA stability of Shq1.Mechanistically,Virma deficiency resulted in decreased m6A modification on Shq1 mRNA,leading to reduced binding ability of m6A-binding protein HNRNPA2B1 with Shq1,thereby decreasing the mRNA stability of Shq1 and reducing its protein expression level.Downregulation of Shq1 inhibited the PI3K/AKT pathway,thereby suppressing cell proliferation and cell cycle progression,ultimately impeding liver regeneration.In summary,our results demonstrate that VIRMA plays a critical role in promoting liver regeneration by regulating m6A modification,providing valuable insights into the epigenetic regulation during liver regeneration.
文摘Background： The recently emerged technology of methylated RNA immunoprecipitation sequencing （MeRIP-seq） sheds light on the study of RNA epigenetics. This new bioinformatics question calls for effective and robust peaking calling algorithms to detect mRNA methylation sites from MeRIP-seq data. Methods： We propose a Bayesian hierarchical model to detect methylation sites from MeRIP-seq data. Our modeling approach includes several important characteristics. First, it models the zero-inflated and over-dispersed counts by deploying a zero-inflated negative binomial model. Second, it incorporates a hidden Markov model （HMM） to account for the spatial dependency of neighboring read enrichment. Third, our Bayesian inference allows the proposed model to borrow strength in parameter estimation, which greatly improves the model stability when dealing with MeRIP-seq data with a small number of replicates. We use Markov chain Monte Carlo （MCMC） algorithms to simultaneously infer the model parameters in a de novo fashion. The R Shiny demo is available at https：//qiwei. shinyapps.io/BaySeqPeak and the R/C ＋＋ code is available at https：//github.com/liqiwei2000/BaySeqPeak. Results： In simulation studies, the proposed method outperformed the competing methods exomePeak and MeTPeak, especially when an excess of zeros were present in the data. In real MeRIP-seq data analysis, the proposed method identified methylation sites that were more consistent with biological knowledge, and had better spatial resolution compared to the other methods. Conclusions： In this study, we develop a Bayesian hierarchical model to identify methylation peaks in MeRIP-seq data. The proposed method has a competitive edge over existing methods in terms of accuracy, robustness and spatial resolution.
