N6-methyladenosine(m6A)is an important RNA methylation modification involved in regulating diverse biological processes across multiple species.Hence,the identification of m6A modification sites provides valuable insi...N6-methyladenosine(m6A)is an important RNA methylation modification involved in regulating diverse biological processes across multiple species.Hence,the identification of m6A modification sites provides valuable insight into the biological mechanisms of complex diseases at the post-transcriptional level.Although a variety of identification algorithms have been proposed recently,most of them capture the features of m6A modification sites by focusing on the sequential dependencies of nucleotides at different positions in RNA sequences,while ignoring the structural dependencies of nucleotides in their threedimensional structures.To overcome this issue,we propose a cross-species end-to-end deep learning model,namely CR-NSSD,which conduct a cross-domain representation learning process integrating nucleotide structural and sequential dependencies for RNA m6A site identification.Specifically,CR-NSSD first obtains the pre-coded representations of RNA sequences by incorporating the position information into single-nucleotide states with chaos game representation theory.It then constructs a crossdomain reconstruction encoder to learn the sequential and structural dependencies between nucleotides.By minimizing the reconstruction and binary cross-entropy losses,CR-NSSD is trained to complete the task of m6A site identification.Extensive experiments have demonstrated the promising performance of CR-NSSD by comparing it with several state-of-the-art m6A identification algorithms.Moreover,the results of cross-species prediction indicate that the integration of sequential and structural dependencies allows CR-NSSD to capture general features of m6A modification sites among different species,thus improving the accuracy of cross-species identification.展开更多
目的研究t(8;21)急性髓系白血病(AML)中AML1-ETO(AE)融合基因与细胞内N6-甲基腺嘌呤(m6A)修饰的关系。方法利用RNA-蛋白免疫共沉淀和高通量测序技术(MeRIP-Seq)在AE(+)和敲除AE的AML细胞系中进行RNAm6A测序,分析整个转录组m6A修饰的变...目的研究t(8;21)急性髓系白血病(AML)中AML1-ETO(AE)融合基因与细胞内N6-甲基腺嘌呤(m6A)修饰的关系。方法利用RNA-蛋白免疫共沉淀和高通量测序技术(MeRIP-Seq)在AE(+)和敲除AE的AML细胞系中进行RNAm6A测序,分析整个转录组m6A修饰的变化。利用高通量测序技术进行转录组测序(RNA-seq)。进一步通过GO分析、KEGG通路富集分析对差异修饰的mRNA进行功能注释。实时荧光定量PCR检测m6A相关酶表达量变化。结果RNAm6A甲基化测序在敲除AE和表达AE的AML细胞系中共检测到26441个基因,包含了72036个m6A peak。AE敲除后细胞内m6A peak的数目由37042个变成34994个,其中有1278个m6A peak升高,1225个下降。AE敲除后新出现了1316个m6A修饰的基因,1830个基因失去了m6A修饰。差异的peak主要在癌症、人类T淋巴细胞白血病病毒Ⅰ等通路中富集。RNA-seq结果显示,AE敲除后有2483个基因表达上调,3913个基因表达下调。MeRIP-Seq和RNA-Seq联合分析结果显示,与非m6A修饰的基因相比,m6A所修饰的基因表达水平均相对较高(SKNO-1:0.6116±1.263 vs 2.010±1.655,P<0.0001;SKNO-1 siAE:0.5528±1.257 vs 2.067±1.686,P<0.0001)。m6A修饰位于3'UTR或5'UTR的基因较位于外显子区的基因表达量更高(SKNO-1:2.177±1.633 vs 1.333±1.470 vs 2.449±1.651,P<0.0001;SKNO-1 siAE:2.304±1.671 vs 1.336±1.522 vs 2.394±1.649,P<0.05)。RNA-seq结果显示,有3种m6A相关酶METTL14、WTAP、ALKBH5的mRNA表达升高(WTAP:5.36±0.5657 vs 13.19±0.3253,METTL14:2.850±0.1556 vs 8.815±1.761,ALKBH5:13.70±0.4596 vs 39.84±6.067,P<0.05)。实时荧光定量PCR检测METTL14、WTAP、ALKBH5的表达量变化发现敲除AE后WTAP、ALKBH5的表达量升高,而METTL14的表达量降低(P<0.05)。结论AE敲除造成m6A相关酶差异,推测AE融合基因或许可以调控一种或多种m6A相关酶的表达控制细胞内的甲基化水平,影响m6A修饰模式。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
基金supported in part by the National Natural Science Foundation of China(62373348)the Natural Science Foundation of Xinjiang Uygur Autonomous Region(2021D01D05)+1 种基金the Tianshan Talent Training Program(2023TSYCLJ0021)the Pioneer Hundred Talents Program of Chinese Academy of Sciences.
文摘N6-methyladenosine(m6A)is an important RNA methylation modification involved in regulating diverse biological processes across multiple species.Hence,the identification of m6A modification sites provides valuable insight into the biological mechanisms of complex diseases at the post-transcriptional level.Although a variety of identification algorithms have been proposed recently,most of them capture the features of m6A modification sites by focusing on the sequential dependencies of nucleotides at different positions in RNA sequences,while ignoring the structural dependencies of nucleotides in their threedimensional structures.To overcome this issue,we propose a cross-species end-to-end deep learning model,namely CR-NSSD,which conduct a cross-domain representation learning process integrating nucleotide structural and sequential dependencies for RNA m6A site identification.Specifically,CR-NSSD first obtains the pre-coded representations of RNA sequences by incorporating the position information into single-nucleotide states with chaos game representation theory.It then constructs a crossdomain reconstruction encoder to learn the sequential and structural dependencies between nucleotides.By minimizing the reconstruction and binary cross-entropy losses,CR-NSSD is trained to complete the task of m6A site identification.Extensive experiments have demonstrated the promising performance of CR-NSSD by comparing it with several state-of-the-art m6A identification algorithms.Moreover,the results of cross-species prediction indicate that the integration of sequential and structural dependencies allows CR-NSSD to capture general features of m6A modification sites among different species,thus improving the accuracy of cross-species identification.
文摘目的研究t(8;21)急性髓系白血病(AML)中AML1-ETO(AE)融合基因与细胞内N6-甲基腺嘌呤(m6A)修饰的关系。方法利用RNA-蛋白免疫共沉淀和高通量测序技术(MeRIP-Seq)在AE(+)和敲除AE的AML细胞系中进行RNAm6A测序,分析整个转录组m6A修饰的变化。利用高通量测序技术进行转录组测序(RNA-seq)。进一步通过GO分析、KEGG通路富集分析对差异修饰的mRNA进行功能注释。实时荧光定量PCR检测m6A相关酶表达量变化。结果RNAm6A甲基化测序在敲除AE和表达AE的AML细胞系中共检测到26441个基因,包含了72036个m6A peak。AE敲除后细胞内m6A peak的数目由37042个变成34994个,其中有1278个m6A peak升高,1225个下降。AE敲除后新出现了1316个m6A修饰的基因,1830个基因失去了m6A修饰。差异的peak主要在癌症、人类T淋巴细胞白血病病毒Ⅰ等通路中富集。RNA-seq结果显示,AE敲除后有2483个基因表达上调,3913个基因表达下调。MeRIP-Seq和RNA-Seq联合分析结果显示,与非m6A修饰的基因相比,m6A所修饰的基因表达水平均相对较高(SKNO-1:0.6116±1.263 vs 2.010±1.655,P<0.0001;SKNO-1 siAE:0.5528±1.257 vs 2.067±1.686,P<0.0001)。m6A修饰位于3'UTR或5'UTR的基因较位于外显子区的基因表达量更高(SKNO-1:2.177±1.633 vs 1.333±1.470 vs 2.449±1.651,P<0.0001;SKNO-1 siAE:2.304±1.671 vs 1.336±1.522 vs 2.394±1.649,P<0.05)。RNA-seq结果显示,有3种m6A相关酶METTL14、WTAP、ALKBH5的mRNA表达升高(WTAP:5.36±0.5657 vs 13.19±0.3253,METTL14:2.850±0.1556 vs 8.815±1.761,ALKBH5:13.70±0.4596 vs 39.84±6.067,P<0.05)。实时荧光定量PCR检测METTL14、WTAP、ALKBH5的表达量变化发现敲除AE后WTAP、ALKBH5的表达量升高,而METTL14的表达量降低(P<0.05)。结论AE敲除造成m6A相关酶差异,推测AE融合基因或许可以调控一种或多种m6A相关酶的表达控制细胞内的甲基化水平,影响m6A修饰模式。
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.
