N6-Methyladenine (6mA)DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes,including the dioot modelArabidopsis thaliana.However,the conservation and divergence of 6mA distri...N6-Methyladenine (6mA)DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes,including the dioot modelArabidopsis thaliana.However,the conservation and divergence of 6mA distribution patterns and functions in plants remain elusive.Here we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars,Nipponbare (Nip;Japonica)and 93-11 (Indica).Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and Arabidopsis.We found that 6mA levels are positively correlated with the expression of key stressrelated genes,which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover,we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants.展开更多
Lingguizhugan Decoction(LGZG)has been investigated in basic studies,with satisfactory effects on insulin resistance in non-alcoholic fatty liver disease(NAFLD).This translational approach aimed to explore the effect a...Lingguizhugan Decoction(LGZG)has been investigated in basic studies,with satisfactory effects on insulin resistance in non-alcoholic fatty liver disease(NAFLD).This translational approach aimed to explore the effect and underlying mechanism of LGZG in clinical setting.A randomized,double-blinded,placebo-controlled trial was performed.A total of 243 eligible participants with NAFLD were equally allocated to receive LGZG(two groups:standard dose and low dose)or placebo for 12 weeks on the basis of lifestyle modifications.The primary efficacy variable was homeostasis model assessment of insulin resistance(HOMA-IR).Analyses were performed in two populations in accordance with body mass index(BMI;overweight/obese,BMI 24 kg/m^(2);lean,BMI<24 kg/m^(2)).For overweight/obese participants,low-dose LGZG significantly decreased their HOMA-IR level compared with placebo(0.19(1.47)versus 0.08(1.99),P=0.038).For lean subjects,neither dose of LGZG showed a superior effect compared with placebo.Methylated DNA immunoprecipitation sequencing and real-time qPCR found that the DNA N6-methyladenine modification levels of protein phosphatase 1 regulatory subunit 3A(PPP1R3A)and autophagy related 3(ATG3)significantly increased after LGZG intervention in overweight/obese population.Low-dose LGZG effectively improved insulin resistance in overweight/obese subjects with NAFLD.The underlying mechanism may be related to the regulation of DNA N6-methyladenine modification of PPP1R3A and ATG3.Lean subjects may not be a targeted population for LGZG.展开更多
BACKGROUND Through experimental research on the biological function of GATA6-AS1,it was confirmed that GATA6-AS1 can inhibit the proliferation,invasion,and migration of gastric cancer cells,suggesting that GATA6-AS1 p...BACKGROUND Through experimental research on the biological function of GATA6-AS1,it was confirmed that GATA6-AS1 can inhibit the proliferation,invasion,and migration of gastric cancer cells,suggesting that GATA6-AS1 plays a role as an anti-oncogene in the occurrence and development of gastric cancer.Further experi-ments confirmed that the overexpression of fat mass and obesity-associated protein(FTO)inhibited the expression of GATA6-AS1,thereby promoting the occurrence and development of gastric cancer.AIM To investigate the effects of GATA6-AS1 on the proliferation,invasion and migration of gastric cancer cells and its mechanism of action.METHODS We used bioinformatics methods to analyze the Cancer Genome Atlas(https://portal.gdc.cancer.gov/.The Cancer Genome Atlas)and download expression data for GATA6-AS1 in gastric cancer tissue and normal tissue.We also constructed a GATA6-AS1 lentivirus overexpression vector which was transfected into gastric cancer cells to investigate its effects on proliferation,migration and invasion,and thereby clarify the expression of GATA6-AS1 in gastric cancer and its biological role in the genesis and development of gastric cancer.Next,we used a database(http://starbase.sysu.edu.cn/starbase2/)to analysis GATA6-AS1 whether by m6A methylation modify regulation and predict the methyltransferases that may methylate GATA6-AS1.Furthermore,RNA immunoprecipitation experiments confirmed that GATA6-AS1 was able to bind to the m6A methylation modification enzyme.These data allowed us to clarify the ability of m6A methylase to influence the action of GATA6-AS1 and its role in the occurrence and development of gastric cancer.RESULTS Low expression levels of GATA6-AS1 were detected in gastric cancer.We also determined the effects of GATA6-AS1 overexpression on the biological function of gastric cancer cells.GATA6-AS1 had strong binding ability with the m6A demethylase FTO,which was expressed at high levels in gastric cancer and negatively correlated with the expression of GATA6-AS1.Following tr展开更多
Chronic myeloid leukemia(CML)is a common adult leukemia.Both the acute phase of the disease and the adverse effects of anti-cancer treatments can lead to a poor prognosis.The N6-methyladenine(m^(6)A)modification plays...Chronic myeloid leukemia(CML)is a common adult leukemia.Both the acute phase of the disease and the adverse effects of anti-cancer treatments can lead to a poor prognosis.The N6-methyladenine(m^(6)A)modification plays an important regulatory role in various physiological and pathological processes.KIAA1429 is a known m^(6)A regulator,but the biological role of KIAA1429 in CML is unclear.In this study,we observed that the m^(6)A levels and KIAA1429 expression were significantly up-regulated in patients with blast phase CML.Notably,KIAA1429 regulated the total level of RNA m^(6)A modification in the CML cells and promoted the malignant biological behaviors of CML cells,including proliferation,migration,and imatinib resistance.Inhibiting KIAA1429 in CML cells reduced the stability of RAB27B mRNA through the m^(6)A/YTHDF1 axis,consequently inhibiting CML proliferation and drug efflux,ultimately increasing the sensitivity of CML cells to imatinib.Moreover,the knockdown of RAB27B also inhibited the proliferation and drug resistance of CML cells and promoted their apoptosis.Rucaparib,a recently developed anti-cancer agent,suppressed the expression of KIAA1429 and CML cell proliferation and promoted cell apoptosis.Rucaparib also inhibited the tumorigenesis of CML cells in vivo.The combined use of rucaparib and imatinib enhanced the sensitivity of CML cells to imatinib.Our study provides evidence that elevated KIAA1429 expression in the blast phase of CML enhances the stability of RAB27B mRNA through the m^(6)A/YTHDF1 axis to up-regulate RAB27B expression,thereby promoting CML progression.Rucaparib exerts inhibitory effects on KIAA1429 expression and thus reduces CML progression.展开更多
Background Diversified histone deacetylation inhibitors(HDACis)have demonstrated encouraging outcomes in multiple malignancies.N6-methyladenine(m6A)is the most prevalent messenger RNA modification that plays an essent...Background Diversified histone deacetylation inhibitors(HDACis)have demonstrated encouraging outcomes in multiple malignancies.N6-methyladenine(m6A)is the most prevalent messenger RNA modification that plays an essential role in the regulation of tumorigenesis.Howbeit,an in-depth understanding of the crosstalk between histone acetylation and m6A RNA modifications remains enigmatic.This study aimed to explore the role of histone acetylation and m6A modifications in the regulation of tumorigenesis of ocular melanoma.Methods Histone modification inhibitor screening was used to explore the effects of HDACis on ocular melanoma cells.Dot blot assay was used to detect the global m6A RNA modification level.Multi-omics assays,including RNA-sequencing,cleavage under targets and tagmentation,single-cell sequencing,methylated RNA immunoprecipitation-sequencing(meRIP-seq),and m6A individual nucleotide resolution cross-linking and immunoprecipitation-sequencing(miCLIP-seq),were performed to reveal the mechanisms of HDACis on methyltransferase-like 14(METTL14)and FAT tumor suppressor homolog 4(FAT4)in ocular melanoma.Quantitative real-time polymerase chain reaction(qPCR),western blotting,and immunofluorescent staining were applied to detect the expression of METTL14 and FAT4 in ocular melanoma cells and tissues.Cell models and orthotopic xenograft models were established to determine the roles of METTL14 and FAT4 in the growth of ocular melanoma.RNA-binding protein immunoprecipitation-qPCR,meRIP-seq,miCLIP-seq,and RNA stability assay were adopted to investigate the mechanism by which m6A levels of FAT4 were affected.Results First,we found that ocular melanoma cells presented vulnerability towards HDACis.HDACis triggered the elevation of m6A RNA modification in ocular melanoma.Further studies revealed that METTL14 served as a downstream candidate for HDACis.METTL14 was silenced by the hypo-histone acetylation status,whereas HDACi restored the normal histone acetylation level of METTL14,thereby inducing its expression.Subsequentl展开更多
BACKGROUND In recent years,the prevalence of Alzheimer’s disease(AD)has increased,which places a great burden on society and families and creates considerable challenges for medical services.N6-methyladenine(m6A)deox...BACKGROUND In recent years,the prevalence of Alzheimer’s disease(AD)has increased,which places a great burden on society and families and creates considerable challenges for medical services.N6-methyladenine(m6A)deoxyribonucleic acid(DNA)adenine methylation is a novel biomarker and is abundant in the brain,but less common in AD.We support to analyze the relationship between DNA m6A and cognition in patients with AD and normal controls(NCs)in China.AIM To analyze the relationship between the novel m6A DNA and cognition in patients with AD and NCs in China.METHODS A total of 179 AD patients(mean age 71.60±9.89 years;males:91;females:88)and 147 NCs(mean age 69.59±11.22 years;males:77;females:70)who were age-and sex-matched were included in our study.All subjects underwent neuropsychological scale assessment and magnetic resonance imaging examination.Apolipoprotein E(APOE)genotypes were measured through agarose gel electrophoresis.Global m6A levels were evaluated by a MethylFlash m6A DNA Methylation ELISA Kit(colorimetric).Global m6A levels in total DNA from ten AD patients with 18F-AV-45(florbetapir)positron emission tomography(PET)positivity and ten NCs with PET negativity were analyzed by dot blotting to determine the results.RESULTS Our ELISA results showed that the global m6A DNA levels in peripheral blood were different between patients with AD and NCs(P=0.002;<0.05).And ten AD patients who were PET positive and ten NCs who were PET negative also showed the same results through dot blotting.There were significant differences between the two groups,which indicated that the leukocyte m6A DNA levels were different(P=0.005;<0.05).The m6A level was approximately 8.33%lower in AD patients than in NCs(mean 0.011±0.006 vs 0.012±0.005).A significant correlation was found between the Montreal Cognitive Assessment score and the peripheral blood m6A level in the tested population(r=0.143,P=0.01;<0.05).However,no relationship was found with APOEε4(P=0.633,>0.05).Further studies should be performed to validate these f展开更多
基金The Ministry of Science and Technology of the People's Republic of China (2016YFD0101001)to X.G.,National Natural Science Foundation of China (31871606,31671670)to X.G.,Recruitment program of Global Youth Expert of China to X.G.,and Fundamental Research funds for Central Non-profit Scientific Institution (1610392017001)to X.G.
文摘N6-Methyladenine (6mA)DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes,including the dioot modelArabidopsis thaliana.However,the conservation and divergence of 6mA distribution patterns and functions in plants remain elusive.Here we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars,Nipponbare (Nip;Japonica)and 93-11 (Indica).Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and Arabidopsis.We found that 6mA levels are positively correlated with the expression of key stressrelated genes,which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover,we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants.
基金This study is supported by the National Natural Science Foundation of China(No.816220108030)the Evidence-based Capacity Building Project for Basic Traditional Chinese Medicine-Specialized Diseases(No.2019XZZX-XH012)Shanghai Three-year Action Planfor Accelerating the Development of Traditional Chinese Medicine(ZY(2018-2020)-CCCX-2002-01).
文摘Lingguizhugan Decoction(LGZG)has been investigated in basic studies,with satisfactory effects on insulin resistance in non-alcoholic fatty liver disease(NAFLD).This translational approach aimed to explore the effect and underlying mechanism of LGZG in clinical setting.A randomized,double-blinded,placebo-controlled trial was performed.A total of 243 eligible participants with NAFLD were equally allocated to receive LGZG(two groups:standard dose and low dose)or placebo for 12 weeks on the basis of lifestyle modifications.The primary efficacy variable was homeostasis model assessment of insulin resistance(HOMA-IR).Analyses were performed in two populations in accordance with body mass index(BMI;overweight/obese,BMI 24 kg/m^(2);lean,BMI<24 kg/m^(2)).For overweight/obese participants,low-dose LGZG significantly decreased their HOMA-IR level compared with placebo(0.19(1.47)versus 0.08(1.99),P=0.038).For lean subjects,neither dose of LGZG showed a superior effect compared with placebo.Methylated DNA immunoprecipitation sequencing and real-time qPCR found that the DNA N6-methyladenine modification levels of protein phosphatase 1 regulatory subunit 3A(PPP1R3A)and autophagy related 3(ATG3)significantly increased after LGZG intervention in overweight/obese population.Low-dose LGZG effectively improved insulin resistance in overweight/obese subjects with NAFLD.The underlying mechanism may be related to the regulation of DNA N6-methyladenine modification of PPP1R3A and ATG3.Lean subjects may not be a targeted population for LGZG.
基金Natural Science Foundation of Shandong Province,No.ZR2020MH207 and No.ZR2020MH251.
文摘BACKGROUND Through experimental research on the biological function of GATA6-AS1,it was confirmed that GATA6-AS1 can inhibit the proliferation,invasion,and migration of gastric cancer cells,suggesting that GATA6-AS1 plays a role as an anti-oncogene in the occurrence and development of gastric cancer.Further experi-ments confirmed that the overexpression of fat mass and obesity-associated protein(FTO)inhibited the expression of GATA6-AS1,thereby promoting the occurrence and development of gastric cancer.AIM To investigate the effects of GATA6-AS1 on the proliferation,invasion and migration of gastric cancer cells and its mechanism of action.METHODS We used bioinformatics methods to analyze the Cancer Genome Atlas(https://portal.gdc.cancer.gov/.The Cancer Genome Atlas)and download expression data for GATA6-AS1 in gastric cancer tissue and normal tissue.We also constructed a GATA6-AS1 lentivirus overexpression vector which was transfected into gastric cancer cells to investigate its effects on proliferation,migration and invasion,and thereby clarify the expression of GATA6-AS1 in gastric cancer and its biological role in the genesis and development of gastric cancer.Next,we used a database(http://starbase.sysu.edu.cn/starbase2/)to analysis GATA6-AS1 whether by m6A methylation modify regulation and predict the methyltransferases that may methylate GATA6-AS1.Furthermore,RNA immunoprecipitation experiments confirmed that GATA6-AS1 was able to bind to the m6A methylation modification enzyme.These data allowed us to clarify the ability of m6A methylase to influence the action of GATA6-AS1 and its role in the occurrence and development of gastric cancer.RESULTS Low expression levels of GATA6-AS1 were detected in gastric cancer.We also determined the effects of GATA6-AS1 overexpression on the biological function of gastric cancer cells.GATA6-AS1 had strong binding ability with the m6A demethylase FTO,which was expressed at high levels in gastric cancer and negatively correlated with the expression of GATA6-AS1.Following tr
基金supported by grants from the National Natural Science Foundation of China(No.81860034,82160405,82160038,82260035)the Natural Science Foundations of Jiangxi Province,China(No.20224BAB216037,20212ACB 206016).
文摘Chronic myeloid leukemia(CML)is a common adult leukemia.Both the acute phase of the disease and the adverse effects of anti-cancer treatments can lead to a poor prognosis.The N6-methyladenine(m^(6)A)modification plays an important regulatory role in various physiological and pathological processes.KIAA1429 is a known m^(6)A regulator,but the biological role of KIAA1429 in CML is unclear.In this study,we observed that the m^(6)A levels and KIAA1429 expression were significantly up-regulated in patients with blast phase CML.Notably,KIAA1429 regulated the total level of RNA m^(6)A modification in the CML cells and promoted the malignant biological behaviors of CML cells,including proliferation,migration,and imatinib resistance.Inhibiting KIAA1429 in CML cells reduced the stability of RAB27B mRNA through the m^(6)A/YTHDF1 axis,consequently inhibiting CML proliferation and drug efflux,ultimately increasing the sensitivity of CML cells to imatinib.Moreover,the knockdown of RAB27B also inhibited the proliferation and drug resistance of CML cells and promoted their apoptosis.Rucaparib,a recently developed anti-cancer agent,suppressed the expression of KIAA1429 and CML cell proliferation and promoted cell apoptosis.Rucaparib also inhibited the tumorigenesis of CML cells in vivo.The combined use of rucaparib and imatinib enhanced the sensitivity of CML cells to imatinib.Our study provides evidence that elevated KIAA1429 expression in the blast phase of CML enhances the stability of RAB27B mRNA through the m^(6)A/YTHDF1 axis to up-regulate RAB27B expression,thereby promoting CML progression.Rucaparib exerts inhibitory effects on KIAA1429 expression and thus reduces CML progression.
基金supported by the National Natural Science Foundation of China(82103240)the Science and Technology Commission of Shanghai(20DZ2270800,23ZR1438400,23ZR1480100 and 23YF1422400)+2 种基金Shanghai Key Clinical Specialty,Shanghai Eye Disease Research Center(2022ZZ01003)Cross-disciplinary Research Fund of Shanghai Ninth People’s Hospital,Shanghai Jiao Tong University(JYJC202210 and YG2023QNB15)Innovative Research Team of High-level Local Universities in Shanghai(SHSMU-ZDCX20210900,SHSMUZDCX20210902).
文摘Background Diversified histone deacetylation inhibitors(HDACis)have demonstrated encouraging outcomes in multiple malignancies.N6-methyladenine(m6A)is the most prevalent messenger RNA modification that plays an essential role in the regulation of tumorigenesis.Howbeit,an in-depth understanding of the crosstalk between histone acetylation and m6A RNA modifications remains enigmatic.This study aimed to explore the role of histone acetylation and m6A modifications in the regulation of tumorigenesis of ocular melanoma.Methods Histone modification inhibitor screening was used to explore the effects of HDACis on ocular melanoma cells.Dot blot assay was used to detect the global m6A RNA modification level.Multi-omics assays,including RNA-sequencing,cleavage under targets and tagmentation,single-cell sequencing,methylated RNA immunoprecipitation-sequencing(meRIP-seq),and m6A individual nucleotide resolution cross-linking and immunoprecipitation-sequencing(miCLIP-seq),were performed to reveal the mechanisms of HDACis on methyltransferase-like 14(METTL14)and FAT tumor suppressor homolog 4(FAT4)in ocular melanoma.Quantitative real-time polymerase chain reaction(qPCR),western blotting,and immunofluorescent staining were applied to detect the expression of METTL14 and FAT4 in ocular melanoma cells and tissues.Cell models and orthotopic xenograft models were established to determine the roles of METTL14 and FAT4 in the growth of ocular melanoma.RNA-binding protein immunoprecipitation-qPCR,meRIP-seq,miCLIP-seq,and RNA stability assay were adopted to investigate the mechanism by which m6A levels of FAT4 were affected.Results First,we found that ocular melanoma cells presented vulnerability towards HDACis.HDACis triggered the elevation of m6A RNA modification in ocular melanoma.Further studies revealed that METTL14 served as a downstream candidate for HDACis.METTL14 was silenced by the hypo-histone acetylation status,whereas HDACi restored the normal histone acetylation level of METTL14,thereby inducing its expression.Subsequentl
基金Supported by the National Key R&D Program of China,No.2016YFC1306300and the National Natural Science Foundation of China,No.81974220.
文摘BACKGROUND In recent years,the prevalence of Alzheimer’s disease(AD)has increased,which places a great burden on society and families and creates considerable challenges for medical services.N6-methyladenine(m6A)deoxyribonucleic acid(DNA)adenine methylation is a novel biomarker and is abundant in the brain,but less common in AD.We support to analyze the relationship between DNA m6A and cognition in patients with AD and normal controls(NCs)in China.AIM To analyze the relationship between the novel m6A DNA and cognition in patients with AD and NCs in China.METHODS A total of 179 AD patients(mean age 71.60±9.89 years;males:91;females:88)and 147 NCs(mean age 69.59±11.22 years;males:77;females:70)who were age-and sex-matched were included in our study.All subjects underwent neuropsychological scale assessment and magnetic resonance imaging examination.Apolipoprotein E(APOE)genotypes were measured through agarose gel electrophoresis.Global m6A levels were evaluated by a MethylFlash m6A DNA Methylation ELISA Kit(colorimetric).Global m6A levels in total DNA from ten AD patients with 18F-AV-45(florbetapir)positron emission tomography(PET)positivity and ten NCs with PET negativity were analyzed by dot blotting to determine the results.RESULTS Our ELISA results showed that the global m6A DNA levels in peripheral blood were different between patients with AD and NCs(P=0.002;<0.05).And ten AD patients who were PET positive and ten NCs who were PET negative also showed the same results through dot blotting.There were significant differences between the two groups,which indicated that the leukocyte m6A DNA levels were different(P=0.005;<0.05).The m6A level was approximately 8.33%lower in AD patients than in NCs(mean 0.011±0.006 vs 0.012±0.005).A significant correlation was found between the Montreal Cognitive Assessment score and the peripheral blood m6A level in the tested population(r=0.143,P=0.01;<0.05).However,no relationship was found with APOEε4(P=0.633,>0.05).Further studies should be performed to validate these f
