Despite the recent advances in the therapeutic modalities,colorectal cancer(CRC)remains to be one of the most common causes of cancer-related death.CRC arises through accumulation of multiple genetic and epigenetic al...Despite the recent advances in the therapeutic modalities,colorectal cancer(CRC)remains to be one of the most common causes of cancer-related death.CRC arises through accumulation of multiple genetic and epigenetic alterations that transform normal colonic epithelium into adenocarcinomas.Among crucial roles of epigenetic alterations,gene silencing by aberrant DNA methylation of promoter regions is one of the most important epigenetic mechanisms.Recent comprehensive methylation analyses on genome-wide scale revealed that sporadic CRC can be classified into distinct epigenotypes.Each epigenotype cooperates with specific genetic alterations,suggesting that they represent different molecular carcinogenic pathways.Precursor lesions of CRC,such as conventional and serrated adenomas,already show similar methylation accumulation to CRC,and can therefore be classified into those epigenotypes of CRC.In addition,specific DNA methylation already occurs in the normal colonic mucosa,which might be utilized for prediction of the personal CRC risk.DNA methylation is suggested to occur at an earlier stage than carcinoma formation,and may predict the molecular basis for future development of CRC.Here,we review DNA methylation and CRC classification,and discuss the possible clinical usefulness of DNA methylation as biomarkers for the diagnosis,prediction of the prognosis and the response to therapy of CRC.展开更多
Two sublines of microalgae Dunaliella viridis Teodor. were obtained: CuS—a subline sensitive to toxic concentration of copper ions and CuR—a subline resistant to toxic concentration of copper ions. The chronological...Two sublines of microalgae Dunaliella viridis Teodor. were obtained: CuS—a subline sensitive to toxic concentration of copper ions and CuR—a subline resistant to toxic concentration of copper ions. The chronological aging of cultures was revealed in increase of DNA (polyploidization) and triacylglycerols (TAG) content in microalgae cells. The adaptation of D. viridis to toxic concentrations of copper ions resulted in formation of an adaptive epygenotype characterized by increased content of carbonylated proteins and decreased content of proline compared to the CuS-subline. The adaptation of D. viridis to toxic concentrations of copper ions resulted in the increase of the rate of chronological aging compared to the CuS-subline. Four subcultures with different rates of transplanting were obtained from each subline. The rate of replicative aging was shown to be dependent on the rate of chronological aging of subcultures (passage rate). The pre-adaptation of D. viridis to toxic concentrations of copper ions was accompanied by increase of accumulation rate of TAG and DNA in cells, which was interpreted as a sign of cellular aging during the progressive passages of the algae culture.展开更多
Inter-and intra-specific variations in phenotype are common and can be associated with genomic mutations as well as epigenomic variation.Profiling both genomic and epigenomic variants is at the core of dissecting phen...Inter-and intra-specific variations in phenotype are common and can be associated with genomic mutations as well as epigenomic variation.Profiling both genomic and epigenomic variants is at the core of dissecting phenotypic variation.However,an efficient targeted genotyping and epigenotyping system is lacking.We describe a new multiplex targeted genotyping and epigenotyping system called improved bulked-PCR sequencing(iBP-seq).We employed iBP-seq for the detection of genotypes and methylation levels of dozens of target regions in mixed DNA samples.iBP-seq can be adapted for the construction of linkage maps,fine mapping of quantitative-trait loci,and detection of genome editing mutations at a cost as low as$0.016 per site per sample.We developed an automated bioinformatics pipeline,including primer design,a series of bioinformatic analyses for genotyping and epigenotyping,and visualization of results.iBP-seq and its bioinformatics pipeline,available at http://zeasystemsbio.hzau.edu.cn/tools/ibp/,can be adapted to a wide variety of species.展开更多
文摘Despite the recent advances in the therapeutic modalities,colorectal cancer(CRC)remains to be one of the most common causes of cancer-related death.CRC arises through accumulation of multiple genetic and epigenetic alterations that transform normal colonic epithelium into adenocarcinomas.Among crucial roles of epigenetic alterations,gene silencing by aberrant DNA methylation of promoter regions is one of the most important epigenetic mechanisms.Recent comprehensive methylation analyses on genome-wide scale revealed that sporadic CRC can be classified into distinct epigenotypes.Each epigenotype cooperates with specific genetic alterations,suggesting that they represent different molecular carcinogenic pathways.Precursor lesions of CRC,such as conventional and serrated adenomas,already show similar methylation accumulation to CRC,and can therefore be classified into those epigenotypes of CRC.In addition,specific DNA methylation already occurs in the normal colonic mucosa,which might be utilized for prediction of the personal CRC risk.DNA methylation is suggested to occur at an earlier stage than carcinoma formation,and may predict the molecular basis for future development of CRC.Here,we review DNA methylation and CRC classification,and discuss the possible clinical usefulness of DNA methylation as biomarkers for the diagnosis,prediction of the prognosis and the response to therapy of CRC.
文摘Two sublines of microalgae Dunaliella viridis Teodor. were obtained: CuS—a subline sensitive to toxic concentration of copper ions and CuR—a subline resistant to toxic concentration of copper ions. The chronological aging of cultures was revealed in increase of DNA (polyploidization) and triacylglycerols (TAG) content in microalgae cells. The adaptation of D. viridis to toxic concentrations of copper ions resulted in formation of an adaptive epygenotype characterized by increased content of carbonylated proteins and decreased content of proline compared to the CuS-subline. The adaptation of D. viridis to toxic concentrations of copper ions resulted in the increase of the rate of chronological aging compared to the CuS-subline. Four subcultures with different rates of transplanting were obtained from each subline. The rate of replicative aging was shown to be dependent on the rate of chronological aging of subcultures (passage rate). The pre-adaptation of D. viridis to toxic concentrations of copper ions was accompanied by increase of accumulation rate of TAG and DNA in cells, which was interpreted as a sign of cellular aging during the progressive passages of the algae culture.
基金the funding supports from the National Natural Science Foundation of China(32272158)the Major Program of Hubei Hongshan Laboratory(2021hszd008)+1 种基金Hainan Yazhou Bay Seed Lab(B21HJ8102)Huazhong Agricultural University Scientific&Technological Self-innovation Foundation(2021ZKPY001)。
文摘Inter-and intra-specific variations in phenotype are common and can be associated with genomic mutations as well as epigenomic variation.Profiling both genomic and epigenomic variants is at the core of dissecting phenotypic variation.However,an efficient targeted genotyping and epigenotyping system is lacking.We describe a new multiplex targeted genotyping and epigenotyping system called improved bulked-PCR sequencing(iBP-seq).We employed iBP-seq for the detection of genotypes and methylation levels of dozens of target regions in mixed DNA samples.iBP-seq can be adapted for the construction of linkage maps,fine mapping of quantitative-trait loci,and detection of genome editing mutations at a cost as low as$0.016 per site per sample.We developed an automated bioinformatics pipeline,including primer design,a series of bioinformatic analyses for genotyping and epigenotyping,and visualization of results.iBP-seq and its bioinformatics pipeline,available at http://zeasystemsbio.hzau.edu.cn/tools/ibp/,can be adapted to a wide variety of species.
