The human genome can be demarcated into domains based on distinct epigenetic states.The trimethylation of histone H3 lysine 9(H3K9me3)is essential for the formation of constitutive heterochromatin nanodomains.However,...The human genome can be demarcated into domains based on distinct epigenetic states.The trimethylation of histone H3 lysine 9(H3K9me3)is essential for the formation of constitutive heterochromatin nanodomains.However,the extent to which genomic regions require specific densities or degrees of H3K9me3 for stable interactions remains unclear.Here,we utilize CRISPR-based DNA imaging to investigate the role of endogenous or ectopic H3K9me3 in chromatin dynamics and genomic interactions.We select three loci(IDR3,TCF3,and PR1)with distinct levels of H3K9me3 to examine the genomic interactions and association with endogenous Heterochromatin Protein 1(HP1α)condensates.Our results demonstrate a positive correlation between the levels of H3K9me3 at the loci and their association with HP1αcondensates.By dual-color labeling and long-term tracking of IDR3 and PR1 loci,we find a periodical association between the two ranging from one to three hours.Epigenetic perturbation-induced Genome organization(EpiGo)-KRAB introduces∼20 kilobases of H3K9me3 at the TCF3 locus,which is sufficient to establish a stable association between TCF3 and HP1αcondensates.In addition,EpiGo-mediated H3K9me3 also leads to stable genomic interaction between IDR3 and TCF3.Briefly,these data suggest that the density of H3K9me3 could dictate the stability of interactions between genomic loci and HP1αcondensates.展开更多
目的检测分析异染色质蛋白1结合蛋白3(heterochromatin protein 1 binding protein 3,HP1BP3)在肝细胞癌中的表达及其对细胞恶性生物学行为的影响。方法应用TCGA数据库分析肝细胞癌与癌旁组织中HP1BP3基因的表达差异。生存检验分析HP1BP...目的检测分析异染色质蛋白1结合蛋白3(heterochromatin protein 1 binding protein 3,HP1BP3)在肝细胞癌中的表达及其对细胞恶性生物学行为的影响。方法应用TCGA数据库分析肝细胞癌与癌旁组织中HP1BP3基因的表达差异。生存检验分析HP1BP3表达与肝细胞癌患者总生存期的关系,单因素及多因素分析相关危险因素。应用Western blot和免疫组化法检测HP1BP3蛋白表达水平。用小干扰RNA(siRNA)分别转染Huh7、HepG2细胞,功能实验检测细胞增殖、迁移和侵袭能力。通过GSEA分析对其作用机制进行探究。结果TCGA数据库分析结果显示,HP1BP3基因在肝细胞癌组织中的表达明显高于非肿瘤组织(P<0.01),高表达组患者的总生存期较低表达组短(P=0.029)。HP1BP3基因是肝细胞癌的独立预测因子(P=0.024)。体外实验结果显示,HP1BP3基因在肝癌细胞株及肝细胞癌组织中表达上调。沉默HP1BP3基因可抑制肝癌细胞的增殖、侵袭和迁移。HP1BP3高表达与泛素化(P<0.001)、核酸切除修复(P<0.001)、RNA降解(P<0.001)、ERBB信号通路(P<0.001)、细胞周期(P<0.001)、细胞凋亡(P<0.001)通路有关。结论HP1BP3基因在肝细胞癌组织中表达上调,是肝细胞癌独立的预后危险因素,可促进肝细胞癌的发生、发展。展开更多
Restricted by the development of the transient flow and solute reactive transport models for unsaturated soil, empirical functions have been used previously to calculate the mass of dissolved or precipitated salt when...Restricted by the development of the transient flow and solute reactive transport models for unsaturated soil, empirical functions have been used previously to calculate the mass of dissolved or precipitated salt when they have to be taken into account. Besides, the solute reactive transport process has often been inferred based on measurements that cost lots of time and manpower. HP1 model coupled with PHREEQC provides a suitable tool to improve the estimation of salt distribution during evaporation in saline soil, where the salt dissolution and precipitation cannot be ignored. In this study, we compare the performance of a standard solute transport(SST) model and the HP1 model to examine the improvement of salt distribution estimation. Model results are compared with experimental data sets from four field lysimeters. These columns were exposed to Na Cl solution with different concentrations(3, 30, 100, and 250 g/L) and were undergoing the same strong evaporation boundary condition. The pre-existing Ca SO_(4), Na Cl and Na2SO_(4)loads were 1.15, 0.47 and 0.23 g/(100 g of soil), respectively. Simulation results show that HP1 ameliorates the overestimation of salt content by SST in deeper soil due to the absence of dissolution of pre-existing soluble salts, and prevents the concentration of the solute from exceeding the solubilities which would occur in SST-result. Additionally, HP1-predicted results can help trace the transport process of each solute. Based on the results, we strongly suggest that the management of fields sensitive to salt content should make use of a coupled flow and chemical reaction model.展开更多
基金This work was funded by the National Natural Science Foundation of China(No.31970591 to H.Ma),the Shanghai Pujiang Program(19PJ1408000 to H.Ma)the Shanghai Science and Technology Innovation Action Plan(21JC1404800 to H.Ma)We thank Luke Lavis(Janelia Research Campus,Howard Hughes Medical Institute,Ashburn,VA,USA)for providing the HaloTag JF-549.U2OS Genomic DNA was a gift from Xingxu Huang.We thank Pengwei Zhang and Shuangli Zhang for their help with cell sorting.
文摘The human genome can be demarcated into domains based on distinct epigenetic states.The trimethylation of histone H3 lysine 9(H3K9me3)is essential for the formation of constitutive heterochromatin nanodomains.However,the extent to which genomic regions require specific densities or degrees of H3K9me3 for stable interactions remains unclear.Here,we utilize CRISPR-based DNA imaging to investigate the role of endogenous or ectopic H3K9me3 in chromatin dynamics and genomic interactions.We select three loci(IDR3,TCF3,and PR1)with distinct levels of H3K9me3 to examine the genomic interactions and association with endogenous Heterochromatin Protein 1(HP1α)condensates.Our results demonstrate a positive correlation between the levels of H3K9me3 at the loci and their association with HP1αcondensates.By dual-color labeling and long-term tracking of IDR3 and PR1 loci,we find a periodical association between the two ranging from one to three hours.Epigenetic perturbation-induced Genome organization(EpiGo)-KRAB introduces∼20 kilobases of H3K9me3 at the TCF3 locus,which is sufficient to establish a stable association between TCF3 and HP1αcondensates.In addition,EpiGo-mediated H3K9me3 also leads to stable genomic interaction between IDR3 and TCF3.Briefly,these data suggest that the density of H3K9me3 could dictate the stability of interactions between genomic loci and HP1αcondensates.
文摘目的检测分析异染色质蛋白1结合蛋白3(heterochromatin protein 1 binding protein 3,HP1BP3)在肝细胞癌中的表达及其对细胞恶性生物学行为的影响。方法应用TCGA数据库分析肝细胞癌与癌旁组织中HP1BP3基因的表达差异。生存检验分析HP1BP3表达与肝细胞癌患者总生存期的关系,单因素及多因素分析相关危险因素。应用Western blot和免疫组化法检测HP1BP3蛋白表达水平。用小干扰RNA(siRNA)分别转染Huh7、HepG2细胞,功能实验检测细胞增殖、迁移和侵袭能力。通过GSEA分析对其作用机制进行探究。结果TCGA数据库分析结果显示,HP1BP3基因在肝细胞癌组织中的表达明显高于非肿瘤组织(P<0.01),高表达组患者的总生存期较低表达组短(P=0.029)。HP1BP3基因是肝细胞癌的独立预测因子(P=0.024)。体外实验结果显示,HP1BP3基因在肝癌细胞株及肝细胞癌组织中表达上调。沉默HP1BP3基因可抑制肝癌细胞的增殖、侵袭和迁移。HP1BP3高表达与泛素化(P<0.001)、核酸切除修复(P<0.001)、RNA降解(P<0.001)、ERBB信号通路(P<0.001)、细胞周期(P<0.001)、细胞凋亡(P<0.001)通路有关。结论HP1BP3基因在肝细胞癌组织中表达上调,是肝细胞癌独立的预后危险因素,可促进肝细胞癌的发生、发展。
基金supported by the National Natural Science Foundation of China (Nos.41572224,U1403282,51709232)the Fundamental Research Funds for the Central Universities,China University of Geosciences (Wuhan) (No.CUG170103)。
文摘Restricted by the development of the transient flow and solute reactive transport models for unsaturated soil, empirical functions have been used previously to calculate the mass of dissolved or precipitated salt when they have to be taken into account. Besides, the solute reactive transport process has often been inferred based on measurements that cost lots of time and manpower. HP1 model coupled with PHREEQC provides a suitable tool to improve the estimation of salt distribution during evaporation in saline soil, where the salt dissolution and precipitation cannot be ignored. In this study, we compare the performance of a standard solute transport(SST) model and the HP1 model to examine the improvement of salt distribution estimation. Model results are compared with experimental data sets from four field lysimeters. These columns were exposed to Na Cl solution with different concentrations(3, 30, 100, and 250 g/L) and were undergoing the same strong evaporation boundary condition. The pre-existing Ca SO_(4), Na Cl and Na2SO_(4)loads were 1.15, 0.47 and 0.23 g/(100 g of soil), respectively. Simulation results show that HP1 ameliorates the overestimation of salt content by SST in deeper soil due to the absence of dissolution of pre-existing soluble salts, and prevents the concentration of the solute from exceeding the solubilities which would occur in SST-result. Additionally, HP1-predicted results can help trace the transport process of each solute. Based on the results, we strongly suggest that the management of fields sensitive to salt content should make use of a coupled flow and chemical reaction model.
