G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. Their structure and function are strongly influenced by their hydration shells. Although...G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. Their structure and function are strongly influenced by their hydration shells. Although extensively studied through various experimental and computational methods, hydration patterns near DNA remain under debate due to the chemically and topologically heterogeneous nature of the exposed surface. In this work, we employed all-atom molecular dynamics(MD) simulation to study the hydration patterns of GQ DNA. The Drude oscillator model was used in MD simulation as a computationally efficient method for modeling electronic polarization in DNA ion solutions. Hydration structure was analyzed in terms of radial distribution functions and high-density three-dimensional hydration sites. Analysis of hydration dynamics focused on self-diffusion rates and orientation time correlation at different structural regions of GQ DNA.The results show highly heterogeneous hydration patterns in both structure and dynamics;for example, there are several insular high-density sites in the inner channel, and ‘spine of water’ in the groove. For water inside the loop, anomalous diffusion is present over a long time scale, but for water around the phosphate group and groove, diffusion becomes normal after ~30 ps. These essentially correspond to deeply buried structural water and strong interaction with DNA, respectively.展开更多
G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of li...G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of linking loops, and the associated metal cations. However, our understanding on the basic physical properties of the formation process and the stability of GQs is rather limited. In this work, we employed ab initio, molecular dynamics(MD), and steered MD(SMD)simulations to study the interaction between loop bases and ions, and the effect on the stability of G-quadruplex DNA, the Drude oscillator model was used in MD and SMD simulations as a computationally efficient manner method for modeling electronic polarization in DNA ion solutions. We observed that the binding energy between DNA bases and ions(K^(+)/Na^(+))is about the base stacking free energies indicates that there will be a competition among the binding of M^(+)-base, H-bonds between bases, and the base-stacking while ions were bound in loop of GQs. Our SMD simulations indicated that the side loop inclined to form the base stacking while the loop sequence was Thy or Ade, and the cross-link loop upon the G-tetrads was not easy to form the base stacking. The base stacking side loop complex K+was found to have a good stabilization synergy. Although a stronger interaction was observed to exist between Cyt and K+, such an interaction was unable to promote the stability of the loop with the sequence Cyt.展开更多
Maternal consumption of a high-fat diet has been linked to increased risks of obesity and impaired glucose metabolism in offspring.However,the precise epigenetic mechanisms governing these intergenerational effects,pa...Maternal consumption of a high-fat diet has been linked to increased risks of obesity and impaired glucose metabolism in offspring.However,the precise epigenetic mechanisms governing these intergenerational effects,particularly during the early stages of offspring development,remain poorly understood.In this study,female C57BL/6J mice were randomly assigned to either a high-fat diet or normal chow diet throughout gestation and lactation.Methylated DNA immunoprecipitation(MeDIP)coupled with microarray analysis was employed to identify differentially methylated genes in the livers of offspring at weaning age.We found that maternal high-fat diet feeding predisposes offspring to obesity and impaired glucose metabolism as early as the weaning period.DNA methylation profile analysis unveiled a significant enrichment of differentially methylated genes within the natural killer(NK)cell-mediated cytotoxicity pathway.MeDIP-PCR validated reduced methylation levels of specific genes within this pathway,including tumour necrosis factorα(TNF-α),phosphoinositide 3-kinase(PI3K),and SHC adaptor protein 1(SHC1).Consistently,the expressions of TNF-α,PI3K,and SHC1 were significantly upregulated,accompanied by elevated serum TNF-αand interleukin-6(IL-6)levels in offspring from dams fed with high-fat diet.Moreover,we assessed the expressions of genes associated with NK cell activities,uncovering a notable rise in hepatic granzyme B levels and a trend towards increased CD107a expression in offspring from dams fed a high-fat diet.In addition,methylation levels of TNF-α,PI3K,and SHC1 promoters were inversely correlated with glucose response during glucose tolerance testing.In conclusion,our findings underscore the critical role of the NK cell-mediated cytotoxicity signaling pathway in mediating DNA methylation patterns,thereby contributing to the programming effects of maternal high-fat diet consumption on offspring glucose metabolism as early as the weaning period.展开更多
Background:Evidence regarding the effectiveness of prenatal nutritional supplements has mainly considered anthropometric pregnancy outcomes.The effect on markers of health and disease,such as offspring telomere length...Background:Evidence regarding the effectiveness of prenatal nutritional supplements has mainly considered anthropometric pregnancy outcomes.The effect on markers of health and disease,such as offspring telomere length(TL)and mitochondrial DNA content(mtDNAc)is unknown.Objectives:We assessed the efficacy of maternal multiple micronutrient(MMN)-fortified balanced-energy protein(BEP)and iron-folic acid(IFA)supplementation on newborn TL as a secondary outcome and mtDNAc as a non-declared outcome.Design:We conducted a randomized controlled trial in rural Burkina Faso,among pregnant females(15-40 years old)enrolled at<21 weeks of gestation.Mothers received either MMN-fortified BEP and IFA(intervention)or IFA only(control)throughout pregnancy.Whole arterial blood samples were collected from the umbilical cord of 104 control and 90 intervention group infants,respectively.Average relative TL and mtDNAc were measured using quantitative polymerase chain reaction.Linear regression models were fitted to assess TL and mtDNAc differences across trial arms.Results:We found that a combined daily MMN-fortified BEP supplement and IFA tablet did not affect newborn TL[β=-0.010(95%CI:-0.057,0.036);P=0.662]or mtDNAc[β=0.065(95%CI:-0.203,0.073);P=0.354],as compared to an IFA tablet alone.These findings were confirmed(P>0.05)by adjusting the regression models for potential prognostic factors of study outcomes at enrollment.Exploratory analyses indicated higher,but non-significantly different mtDNAc among children born either small-for-gestational age,low birthweight,or preterm.Conclusion:Newborns from mothers who received daily nutritional supplements across gestation did not have different relative TL or mtDNAc.展开更多
基金supported by the National Natural Science Foundation of China (Grant Nos. 11705160 and 11647074)。
文摘G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. Their structure and function are strongly influenced by their hydration shells. Although extensively studied through various experimental and computational methods, hydration patterns near DNA remain under debate due to the chemically and topologically heterogeneous nature of the exposed surface. In this work, we employed all-atom molecular dynamics(MD) simulation to study the hydration patterns of GQ DNA. The Drude oscillator model was used in MD simulation as a computationally efficient method for modeling electronic polarization in DNA ion solutions. Hydration structure was analyzed in terms of radial distribution functions and high-density three-dimensional hydration sites. Analysis of hydration dynamics focused on self-diffusion rates and orientation time correlation at different structural regions of GQ DNA.The results show highly heterogeneous hydration patterns in both structure and dynamics;for example, there are several insular high-density sites in the inner channel, and ‘spine of water’ in the groove. For water inside the loop, anomalous diffusion is present over a long time scale, but for water around the phosphate group and groove, diffusion becomes normal after ~30 ps. These essentially correspond to deeply buried structural water and strong interaction with DNA, respectively.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11705160 and 11647074)。
文摘G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of linking loops, and the associated metal cations. However, our understanding on the basic physical properties of the formation process and the stability of GQs is rather limited. In this work, we employed ab initio, molecular dynamics(MD), and steered MD(SMD)simulations to study the interaction between loop bases and ions, and the effect on the stability of G-quadruplex DNA, the Drude oscillator model was used in MD and SMD simulations as a computationally efficient manner method for modeling electronic polarization in DNA ion solutions. We observed that the binding energy between DNA bases and ions(K^(+)/Na^(+))is about the base stacking free energies indicates that there will be a competition among the binding of M^(+)-base, H-bonds between bases, and the base-stacking while ions were bound in loop of GQs. Our SMD simulations indicated that the side loop inclined to form the base stacking while the loop sequence was Thy or Ade, and the cross-link loop upon the G-tetrads was not easy to form the base stacking. The base stacking side loop complex K+was found to have a good stabilization synergy. Although a stronger interaction was observed to exist between Cyt and K+, such an interaction was unable to promote the stability of the loop with the sequence Cyt.
基金sponsored by National Natural Science Foundation of China(81800703)Postdoctoral Fellowship Program of China Postdoctoral Science Foundation(GZC20231088)+8 种基金Beijing Nova Program(Z201100006820117 and 20220484181)Beijing Municipal Natural Science Foundation(7184252)the Fundamental Research Funds for the Central Universitiesthe Fundamental Research Funds for the Central Universities(BMU2021MX013)Peking University Clinical Scientist Training Program(BMU2023PYJH022)Peking University Medicine Seed Fund for Interdisciplinary ResearchChina Endocrine and Metabolism Young Scientific Talent Research Project(2022-N-02-01)China Diabetes Young Scientific Talent Research ProjectBethune-Merck Diabetes Research Fund of Bethune Charitable Foundation。
文摘Maternal consumption of a high-fat diet has been linked to increased risks of obesity and impaired glucose metabolism in offspring.However,the precise epigenetic mechanisms governing these intergenerational effects,particularly during the early stages of offspring development,remain poorly understood.In this study,female C57BL/6J mice were randomly assigned to either a high-fat diet or normal chow diet throughout gestation and lactation.Methylated DNA immunoprecipitation(MeDIP)coupled with microarray analysis was employed to identify differentially methylated genes in the livers of offspring at weaning age.We found that maternal high-fat diet feeding predisposes offspring to obesity and impaired glucose metabolism as early as the weaning period.DNA methylation profile analysis unveiled a significant enrichment of differentially methylated genes within the natural killer(NK)cell-mediated cytotoxicity pathway.MeDIP-PCR validated reduced methylation levels of specific genes within this pathway,including tumour necrosis factorα(TNF-α),phosphoinositide 3-kinase(PI3K),and SHC adaptor protein 1(SHC1).Consistently,the expressions of TNF-α,PI3K,and SHC1 were significantly upregulated,accompanied by elevated serum TNF-αand interleukin-6(IL-6)levels in offspring from dams fed with high-fat diet.Moreover,we assessed the expressions of genes associated with NK cell activities,uncovering a notable rise in hepatic granzyme B levels and a trend towards increased CD107a expression in offspring from dams fed a high-fat diet.In addition,methylation levels of TNF-α,PI3K,and SHC1 promoters were inversely correlated with glucose response during glucose tolerance testing.In conclusion,our findings underscore the critical role of the NK cell-mediated cytotoxicity signaling pathway in mediating DNA methylation patterns,thereby contributing to the programming effects of maternal high-fat diet consumption on offspring glucose metabolism as early as the weaning period.
基金supported by the Bill&Melinda Gates Foundation(OPP1175213)supported by the Research Foundation Flanders(12X9620N and 12X9623N)the European Research Council(ERC)under the European Union’s Horizon 2020 research and innovation program(946192,HUMYCO)。
文摘Background:Evidence regarding the effectiveness of prenatal nutritional supplements has mainly considered anthropometric pregnancy outcomes.The effect on markers of health and disease,such as offspring telomere length(TL)and mitochondrial DNA content(mtDNAc)is unknown.Objectives:We assessed the efficacy of maternal multiple micronutrient(MMN)-fortified balanced-energy protein(BEP)and iron-folic acid(IFA)supplementation on newborn TL as a secondary outcome and mtDNAc as a non-declared outcome.Design:We conducted a randomized controlled trial in rural Burkina Faso,among pregnant females(15-40 years old)enrolled at<21 weeks of gestation.Mothers received either MMN-fortified BEP and IFA(intervention)or IFA only(control)throughout pregnancy.Whole arterial blood samples were collected from the umbilical cord of 104 control and 90 intervention group infants,respectively.Average relative TL and mtDNAc were measured using quantitative polymerase chain reaction.Linear regression models were fitted to assess TL and mtDNAc differences across trial arms.Results:We found that a combined daily MMN-fortified BEP supplement and IFA tablet did not affect newborn TL[β=-0.010(95%CI:-0.057,0.036);P=0.662]or mtDNAc[β=0.065(95%CI:-0.203,0.073);P=0.354],as compared to an IFA tablet alone.These findings were confirmed(P>0.05)by adjusting the regression models for potential prognostic factors of study outcomes at enrollment.Exploratory analyses indicated higher,but non-significantly different mtDNAc among children born either small-for-gestational age,low birthweight,or preterm.Conclusion:Newborns from mothers who received daily nutritional supplements across gestation did not have different relative TL or mtDNAc.
