Electron microscopic autoradiographic studies on the dynamics and location of DNAsynthesis by means of incorporation of ~8H-thymidine during the replication of duck plaguevirus (DPV) revealed that the duration of DNA ...Electron microscopic autoradiographic studies on the dynamics and location of DNAsynthesis by means of incorporation of ~8H-thymidine during the replication of duck plaguevirus (DPV) revealed that the duration of DNA synthesis of DPV was rather long. The repli-cation of viral DNA occurred simultaneously with the assembly procedure of nucleocapsids, thematuration and release of viruses. DNA synthesis of DPV occurred in the matrix with lowerelectron density in the nucleus. The replicated viral DNA accumulated in the viroplast With highelectron density where the assembly of nucleocapsids occurred. The viroplast with high electrondensity was not the region of viral DNA synthesis.展开更多
The migrating TdT<sup>+</sup> thymocytes can die in other tissues, promoting the surrounding cells’ renewing likes holocrine secretion does. To clarify the role of TdT-enzyme for this function of progenit...The migrating TdT<sup>+</sup> thymocytes can die in other tissues, promoting the surrounding cells’ renewing likes holocrine secretion does. To clarify the role of TdT-enzyme for this function of progenitor lymphocytes, their extracellular media with its components included by living cells analyzed <em>in vitro</em> before and after<em> in vivo</em> irradiation of donor rats. The nucleoid with DNase-sensitive (free) DNA and TdT activity discovered in extracellular media conditioned preliminary by spontaneous apoptotic death of a minor part of the thymocyte’s suspension <em>in vitro</em>. The penetration of labeled products of non-template synthesis with free DNA’ primers from media into cells by pinocytosis confirmed by exogenous polymeric DNA marked artificially. The DNA penetration into cells follows an increase of the cell’s viability and acceleration of spontaneous intracellular DNA-synthesis controlled with labeled thymidine uptake. Both phenomena are typical for either the lowest initial concentration of intact cells or their preliminary irradiation <em>in vivo</em>. The data point to possible involvement of apoptotic decay of TdT<sup>+</sup> cells in the reutilization of the extracellular DNA fragments for reparation/regeneration of surrounding living cells.展开更多
Despite continuous improvements,it is difficult to efficiently amplify large sequences from complex templates using current PCR methods.Here,we developed a suppression thermo-interlaced(STI)PCR method for the efficien...Despite continuous improvements,it is difficult to efficiently amplify large sequences from complex templates using current PCR methods.Here,we developed a suppression thermo-interlaced(STI)PCR method for the efficient and specific amplification of long DNA sequences from genomes and synthetic DNA pools.This method uses site-specific primers containing a common 50 tag to generate a stem-loop structure,thereby repressing the amplification of smaller non-specific products through PCR suppression(PS).However,large target products are less affected by PS and show enhanced amplification when the competitive amplification of non-specific products is suppressed.Furthermore,this method uses nested thermointerlaced cycling with varied temperatures to optimize strand extension of long sequences with an uneven GC distribution.The combination of these two factors in STI PCR produces a multiplier effect,markedly increasing specificity and amplification capacity.We also developed a webtool,calGC,for analyzing the GC distribution of target DNA sequences and selecting suitable thermo-cycling programs for STI PCR.Using this method,we stably amplified very long genomic fragments(up to 38 kb)from plants and human and greatly increased the length of de novo DNA synthesis,which has many applications such as cloning,expression,and targeted genomic sequencing.Our method greatly extends PCR capacity and has great potential for use in biological fields.展开更多
DNA synthesis and collagen formations on the implant material by cell culture in vitro are the most important phenotypical expression to estimate the biocompatibility. In this part, DNA synthesis and collagen formatio...DNA synthesis and collagen formations on the implant material by cell culture in vitro are the most important phenotypical expression to estimate the biocompatibility. In this part, DNA synthesis and collagen formation on implant materials were quantitatively and qualitatively estimated by radioactive isotope H + thymidine to incorporate into DNA chains, H + proline to incorporate into type I collagen proteins followed by scin tillation counting and antibody antigen immunocytochemistry staining, respectively. Research results demonstrate that hydroxyapatite (HA) stimulates DNA synthesis and collagen formation on the material whereas this stimulation is restricted by adding spinel to the materials. There are statistical differences between the influences of material components on both DNA synthesis and collagen formation. It is supposed that porous materials can supply more platforms for cell anchoring, and more DNA and collagen are synthesised on the porous materials. Immersion in culture medium results in new HA crystal formation on the porous HA materials.展开更多
Synthetic genomics has provided new bottom-up platforms for the functional study of viral and microbial genomes.The construction of the large,gigabase(Gb)-sized genomes of higher organisms will deepen our understandin...Synthetic genomics has provided new bottom-up platforms for the functional study of viral and microbial genomes.The construction of the large,gigabase(Gb)-sized genomes of higher organisms will deepen our understanding of genetic blueprints significantly.But for the synthesis and assembly of such large-scale genomes,the development of new or expanded methods is required.In this study,we develop an efficient pipeline for the construction of large DNA fragments sized 100 kilobases(kb)or above from scratches and describe an efficient method for“scar-free”engineering of the assembled sequences.Our method,therefore,should provide a standard framework for producing long DNA molecules,which are critical materials for synthetic genomics and metabolic engineering.展开更多
N^(6)-methyldeoxyadenosine(6 mdA) modification is considered as a new epigenetic mark that may play important roles in various biological processes.However,it remains unclear about the effect of 6 mdA on DNA replicati...N^(6)-methyldeoxyadenosine(6 mdA) modification is considered as a new epigenetic mark that may play important roles in various biological processes.However,it remains unclear about the effect of 6 mdA on DNA replication in human cells.Herein,we combined next-generation sequencing with shuttle vector technology to explore how 6 mdA affects the efficiency and accuracy of DNA replication in human cells.Our results showed that 6 mdA neither blocked DNA replication nor induced mutations in human cells.Moreover,we found that the depletion of translesion synthesis DNA polymerase(Pol) κ,Pol η,Pol ι or Pol ζ did not significantly change the biological consequences of 6 mdA during replication in human cells.The negligible impact of 6 mdA on DNA replication is consistent with its potential role in epigenetic gene expression.展开更多
In addition to DNA repair pathways,cells utilize translesion DNA synthesis(TLS)to bypass DNA lesions during replication.During TLS,Y-family DNA polymerase(Polη,Polκ,Polιand Rev1)inserts specific nucleotide opposite...In addition to DNA repair pathways,cells utilize translesion DNA synthesis(TLS)to bypass DNA lesions during replication.During TLS,Y-family DNA polymerase(Polη,Polκ,Polιand Rev1)inserts specific nucleotide opposite preferred DNA lesions,and then Polζ consisting of two subunits,Rev3 and Rev7,carries out primer extension.Here,we report the complex structures of Rev3-Rev7-Rev1^(CTD) and Rev3-Rev7-Rev1^(CTD)-Polκ^(RIR).These two structures demonstrate that Rev1^(CTD) contains separate binding sites for Polκand Rev7.Our BIAcore experiments provide additional support for the notion that the interaction between Rev3 and Rev7 increases the affinity of Rev7 and Rev1.We also verified through FRET experiment that Rev1,Rev3,Rev7 and Polκ form a stable quaternary complex in vivo,thereby suggesting an efficient switching mechanism where the“inserter”polymerase can be immediately replaced by an“extender”polymerase within the same quaternary complex.展开更多
Aim:The transcription factor RIP140(receptor interacting protein of 140 kDa)is involved in intestinal tumorigenesis.It plays a role in the control of microsatellite instability(MSI),through the regulation of MSH2 and ...Aim:The transcription factor RIP140(receptor interacting protein of 140 kDa)is involved in intestinal tumorigenesis.It plays a role in the control of microsatellite instability(MSI),through the regulation of MSH2 and MSH6 gene expression.The aim of this study was to explore its effect on the expression of POLK,the gene encoding the specialized translesion synthesis(TLS)DNA polymeraseκknown to perform accurate DNA synthesis at microsatellites.Methods:Different mouse models and engineered human colorectal cancer(CRC)cell lines were used to analyze by RT-qPCR,while Western blotting and luciferase assays were used to elucidate the role of RIP140 on POLK gene expression.Published DNA microarray datasets were reanalyzed.The in vitro sensitivity of CRC cells to methyl methane sulfonate and cisplatin was determined.Results:RIP140 positively regulates,at the transcriptional level,the expression of the POLK gene,and this effect involves,at least partly,the p53 tumor suppressor.In different cohorts of CRC biopsies(with or without MSI),a strong positive correlation was observed between RIP140 and POLK gene expression.In connection with its effect on POLK levels and the TLS function of this polymerase,the cellular response to methyl methane sulfonate was increased in cells lacking the Rip140 gene.Finally,the association of RIP140 expression with better overall survival of CRC patients was observed only when the corresponding tumors exhibited low levels of POLK,thus strengthening the functional link between the two genes in human CRC.Conclusion:The regulation of POLK gene expression by RIP140 could thus contribute to the maintenance of microsatellite stability,and more generally to the control of genome integrity.展开更多
文摘Electron microscopic autoradiographic studies on the dynamics and location of DNAsynthesis by means of incorporation of ~8H-thymidine during the replication of duck plaguevirus (DPV) revealed that the duration of DNA synthesis of DPV was rather long. The repli-cation of viral DNA occurred simultaneously with the assembly procedure of nucleocapsids, thematuration and release of viruses. DNA synthesis of DPV occurred in the matrix with lowerelectron density in the nucleus. The replicated viral DNA accumulated in the viroplast With highelectron density where the assembly of nucleocapsids occurred. The viroplast with high electrondensity was not the region of viral DNA synthesis.
文摘The migrating TdT<sup>+</sup> thymocytes can die in other tissues, promoting the surrounding cells’ renewing likes holocrine secretion does. To clarify the role of TdT-enzyme for this function of progenitor lymphocytes, their extracellular media with its components included by living cells analyzed <em>in vitro</em> before and after<em> in vivo</em> irradiation of donor rats. The nucleoid with DNase-sensitive (free) DNA and TdT activity discovered in extracellular media conditioned preliminary by spontaneous apoptotic death of a minor part of the thymocyte’s suspension <em>in vitro</em>. The penetration of labeled products of non-template synthesis with free DNA’ primers from media into cells by pinocytosis confirmed by exogenous polymeric DNA marked artificially. The DNA penetration into cells follows an increase of the cell’s viability and acceleration of spontaneous intracellular DNA-synthesis controlled with labeled thymidine uptake. Both phenomena are typical for either the lowest initial concentration of intact cells or their preliminary irradiation <em>in vivo</em>. The data point to possible involvement of apoptotic decay of TdT<sup>+</sup> cells in the reutilization of the extracellular DNA fragments for reparation/regeneration of surrounding living cells.
基金supported by the National Natural Science Foundation of China(31991222,32030080 and 31760300)the Key Research Program of the Guangzhou Science,Technology and Innovation Commission(201904020030)+1 种基金the Major Program of Guangdong Basic and Applied Basic Research(2019B030302006)the China Postdoctoral Science Foundation(2020M682730).
文摘Despite continuous improvements,it is difficult to efficiently amplify large sequences from complex templates using current PCR methods.Here,we developed a suppression thermo-interlaced(STI)PCR method for the efficient and specific amplification of long DNA sequences from genomes and synthetic DNA pools.This method uses site-specific primers containing a common 50 tag to generate a stem-loop structure,thereby repressing the amplification of smaller non-specific products through PCR suppression(PS).However,large target products are less affected by PS and show enhanced amplification when the competitive amplification of non-specific products is suppressed.Furthermore,this method uses nested thermointerlaced cycling with varied temperatures to optimize strand extension of long sequences with an uneven GC distribution.The combination of these two factors in STI PCR produces a multiplier effect,markedly increasing specificity and amplification capacity.We also developed a webtool,calGC,for analyzing the GC distribution of target DNA sequences and selecting suitable thermo-cycling programs for STI PCR.Using this method,we stably amplified very long genomic fragments(up to 38 kb)from plants and human and greatly increased the length of de novo DNA synthesis,which has many applications such as cloning,expression,and targeted genomic sequencing.Our method greatly extends PCR capacity and has great potential for use in biological fields.
文摘DNA synthesis and collagen formations on the implant material by cell culture in vitro are the most important phenotypical expression to estimate the biocompatibility. In this part, DNA synthesis and collagen formation on implant materials were quantitatively and qualitatively estimated by radioactive isotope H + thymidine to incorporate into DNA chains, H + proline to incorporate into type I collagen proteins followed by scin tillation counting and antibody antigen immunocytochemistry staining, respectively. Research results demonstrate that hydroxyapatite (HA) stimulates DNA synthesis and collagen formation on the material whereas this stimulation is restricted by adding spinel to the materials. There are statistical differences between the influences of material components on both DNA synthesis and collagen formation. It is supposed that porous materials can supply more platforms for cell anchoring, and more DNA and collagen are synthesised on the porous materials. Immersion in culture medium results in new HA crystal formation on the porous HA materials.
基金supported by the National Key Research and Development Program of China(2018YFA0900100 and 2019YFA0903800)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDPB18)+3 种基金the National Natural Science Foundation of China(31800069,32030004,31725002 and 32001065)Shenzhen Science and Technology Program(KQTD20180413181837372)Guangdong Provincial Key Laboratory of Synthetic Genomics(2019B030301006)Shenzhen Outstanding Talents Training Fund and the CAS President’s International Fellowship Initiative(2021VBB0002)。
文摘Synthetic genomics has provided new bottom-up platforms for the functional study of viral and microbial genomes.The construction of the large,gigabase(Gb)-sized genomes of higher organisms will deepen our understanding of genetic blueprints significantly.But for the synthesis and assembly of such large-scale genomes,the development of new or expanded methods is required.In this study,we develop an efficient pipeline for the construction of large DNA fragments sized 100 kilobases(kb)or above from scratches and describe an efficient method for“scar-free”engineering of the assembled sequences.Our method,therefore,should provide a standard framework for producing long DNA molecules,which are critical materials for synthetic genomics and metabolic engineering.
基金supported by the National Natural Science Foundation of China (Nos. 21807030, 21907028)the Science and Technology Innovation Program of Hunan Province(No. 2019RS2020)+1 种基金Natural Science Foundation of Hunan Province(No. 2020JJ5046)the Fundamental Research Funds for the Central Universities (Nos. 531118010061, 531118010259)。
文摘N^(6)-methyldeoxyadenosine(6 mdA) modification is considered as a new epigenetic mark that may play important roles in various biological processes.However,it remains unclear about the effect of 6 mdA on DNA replication in human cells.Herein,we combined next-generation sequencing with shuttle vector technology to explore how 6 mdA affects the efficiency and accuracy of DNA replication in human cells.Our results showed that 6 mdA neither blocked DNA replication nor induced mutations in human cells.Moreover,we found that the depletion of translesion synthesis DNA polymerase(Pol) κ,Pol η,Pol ι or Pol ζ did not significantly change the biological consequences of 6 mdA during replication in human cells.The negligible impact of 6 mdA on DNA replication is consistent with its potential role in epigenetic gene expression.
基金supported financially by the National Basic Research Program(973 Program)(No.2011CB910302)the National Natural Science Foundation of China(Grant Nos.31025009,31021062 and 31200558).
文摘In addition to DNA repair pathways,cells utilize translesion DNA synthesis(TLS)to bypass DNA lesions during replication.During TLS,Y-family DNA polymerase(Polη,Polκ,Polιand Rev1)inserts specific nucleotide opposite preferred DNA lesions,and then Polζ consisting of two subunits,Rev3 and Rev7,carries out primer extension.Here,we report the complex structures of Rev3-Rev7-Rev1^(CTD) and Rev3-Rev7-Rev1^(CTD)-Polκ^(RIR).These two structures demonstrate that Rev1^(CTD) contains separate binding sites for Polκand Rev7.Our BIAcore experiments provide additional support for the notion that the interaction between Rev3 and Rev7 increases the affinity of Rev7 and Rev1.We also verified through FRET experiment that Rev1,Rev3,Rev7 and Polκ form a stable quaternary complex in vivo,thereby suggesting an efficient switching mechanism where the“inserter”polymerase can be immediately replaced by an“extender”polymerase within the same quaternary complex.
文摘Aim:The transcription factor RIP140(receptor interacting protein of 140 kDa)is involved in intestinal tumorigenesis.It plays a role in the control of microsatellite instability(MSI),through the regulation of MSH2 and MSH6 gene expression.The aim of this study was to explore its effect on the expression of POLK,the gene encoding the specialized translesion synthesis(TLS)DNA polymeraseκknown to perform accurate DNA synthesis at microsatellites.Methods:Different mouse models and engineered human colorectal cancer(CRC)cell lines were used to analyze by RT-qPCR,while Western blotting and luciferase assays were used to elucidate the role of RIP140 on POLK gene expression.Published DNA microarray datasets were reanalyzed.The in vitro sensitivity of CRC cells to methyl methane sulfonate and cisplatin was determined.Results:RIP140 positively regulates,at the transcriptional level,the expression of the POLK gene,and this effect involves,at least partly,the p53 tumor suppressor.In different cohorts of CRC biopsies(with or without MSI),a strong positive correlation was observed between RIP140 and POLK gene expression.In connection with its effect on POLK levels and the TLS function of this polymerase,the cellular response to methyl methane sulfonate was increased in cells lacking the Rip140 gene.Finally,the association of RIP140 expression with better overall survival of CRC patients was observed only when the corresponding tumors exhibited low levels of POLK,thus strengthening the functional link between the two genes in human CRC.Conclusion:The regulation of POLK gene expression by RIP140 could thus contribute to the maintenance of microsatellite stability,and more generally to the control of genome integrity.
