Heterosis and polyploidy have an overwhelming influence on plant evolution.Recently,polyploid rice hybrids have been used to breed new rice varieties because they combine the advantages of both heterosis and polyploid...Heterosis and polyploidy have an overwhelming influence on plant evolution.Recently,polyploid rice hybrids have been used to breed new rice varieties because they combine the advantages of both heterosis and polyploidy.In this study,we generated six rice lines:autotetraploid rice hybrids and their autotetraploid parents,diploid donors,and hybrids of the diploid donors.To investigate the molecular mechanism controlling the effects of both hybridization and polyploidization,we performed bisulfite and RNA sequencing on young panicles at the pollen meiosis stage to compare the DNA metabolomes and transcriptomes among the six rice lines.The hybrids lines were hypermethylated compared to their corresponding parents and the autotetraploid lines showed globally increased DNA methylation of their transposable elements compared to the diploid donors.The alteration in DNA methylation level corresponded to the differential gene expressions among the rice genotypes,suggesting that methylation changes induced by polyploidization and hybridization may affect gene expression.Groups of gene candidates were identified that may be associated with heterosis and polyploidy.Our results provide DNA information that can be used to investigate epigenetic modification during heterosis and polyploidy in rice.展开更多
Previous studies have shown rapid and extensive genomic However, these studies are based on either a few pre-selected instability associated with early stages of allopolyploidization in wheat. genomic loci or genome-w...Previous studies have shown rapid and extensive genomic However, these studies are based on either a few pre-selected instability associated with early stages of allopolyploidization in wheat. genomic loci or genome-wide analysis of a single plant individual for a given cross combination, thus making the extent and generality of the changes uncertain. To further study the generality and characteristics of allopolyploidization-induced genomic instability in wheat, we investigated genetic and epigenetic changes from a genome-wide perspective (by using the AFLP and MSAP markers) in four sets of newly synthesized allotetraploid wheat lines with various genome constitutions, each containing three randomly chosen individual plants at the same generation. We document that although general chromosomal stability was characteristic of all four sets of allotetraploid wheat lines, genetic and epigenetic changes at the molecular level occurred in all these plants, with both kinds of changes classifiable into two distinct categories, i.e., stochastic and directed. The abundant type of genetic change is loss of parental bands while the prevalent cytosine methylation pattern alteration is hypermethylation at the CHG sites. Our results have extended previous studies regarding allopolyploidization-induced genomic dynamics in wheat by demonstrafing the generality of both genetic and epigenetic changes associated with multiple nascent allotetraploid wheat lines, and providing novel insights into the characteristics of the two kinds of induced genomic instabilities.展开更多
In 2020,the International Agency for Research on Cancer and the World Health Organization's GLOBOCAN database ranked colorectal cancer(CRC)as the third most common cancer in the world.Most cases of CRC(>95%)are...In 2020,the International Agency for Research on Cancer and the World Health Organization's GLOBOCAN database ranked colorectal cancer(CRC)as the third most common cancer in the world.Most cases of CRC(>95%)are sporadic and develop from colorectal polyps that can progress to intramucosal carcinoma and CRC.Increasing evidence is accumulating that the gut microbiota can play a key role in the initiation and progression of CRC,as well as in the treatment of CRC,acting as an important metabolic and immunological regulator.Factors that may determine the microbiota role in CRC carcinogenesis include inflammation,changes in intestinal stem cell function,impact of bacterial metabolites on gut mucosa,accumulation of genetic mutations and other factors.In this review,I discuss the major mechanisms of the development of sporadic CRC,provide detailed characteristics of the bacteria that are most often associated with CRC,and analyze the role of the microbiome and microbial metabolites in inflammation initiation,activation of proliferative activity in intestinal epithelial and stem cells,and the development of genetic and epigenetic changes in CRC.I consider longterm studies in this direction to be very important,as they open up new opportunities for the treatment and prevention of CRC.展开更多
Hepatitis C virus(HCV)chronic infection is associated with fibrosis progression,end-stage liver complications and HCC.Not surprisingly,HCV infection is a leading cause of liver-related morbidity and mortality worldwid...Hepatitis C virus(HCV)chronic infection is associated with fibrosis progression,end-stage liver complications and HCC.Not surprisingly,HCV infection is a leading cause of liver-related morbidity and mortality worldwide.After sustained virological response(SVR),the risk of developing hepatocellular carcinoma is not completely eliminated in patients with established cirrhosis or with advanced fibrosis.Therefore,lifelong surveillance is currently recommended.This strategy is likely not universally cost-effective and harmless,considering that not all patients with advanced fibrosis have the same risk of developing HCC.Factors related to the severity of liver disease and its potential to improve after SVR,the molecular and epigenetic changes that occur during infection and other associated comorbidities might account for different risk levels and are likely essential for identifying patients who would benefit from screening programs after SVR.Efforts to develop predictive models and risk calculators,biomarkers and genetic panels and even deep learning models to estimate the individual risk of HCC have been made in the direct-acting antiviral agents era,when thousands of patients with advanced fibrosis and cirrhosis have reached SVR.These tools could help to identify patients with very low HCC risk in whom surveillance might not be justified.In this review,factors affecting the probability of HCC development after SVR,the benefits and risks of surveillance,suggested strategies to estimate individualized HCC risk and the current evidence to recommend lifelong surveillance are discussed.展开更多
Nowadays,it is clear that adult stem cells,also called as tissue stem cells,play a central role to repair and maintain the tissue in which they reside by their selfrenewal ability and capacity of differentiating into ...Nowadays,it is clear that adult stem cells,also called as tissue stem cells,play a central role to repair and maintain the tissue in which they reside by their selfrenewal ability and capacity of differentiating into distinct and specialized cells.As stem cells age,their renewal ability declines and their capacity to maintain organ homeostasis and regeneration is impaired.From a molecular perspective,these changes in stem cells properties can be due to several types of cell intrinsic injury and DNA aberrant alteration(i.e epigenomic profile)as well as changes in the tissue microenviroment,both into the niche and by systemic circulating factors.Strikingly,it has been suggested that aging-induced deterioration of stem cell functions may play a key role in the pathophysiology of the various agingassociated disorders.Therefore,understanding how resident stem cell age and affects near and distant tissues is fundamental.Here,we examine the current knowledge about aging mechanisms in several kinds of adult stem cells under physiological and pathological conditions and the principal aging-related changes in number,function and phenotype that determine the loss of tissue renewal properties.Furthermore,we examine the possible cell rejuvenation strategies.Stem cell rejuvenation may reverse the aging phenotype and the discovery of effective methods for inducing and differentiating pluripotent stem cells for cell replacement therapies could open up new possibilities for treating age-related diseases.展开更多
RNA viruses cause a multitude of human diseases,including several pandemic events in the past century.Upon viral invasion,the innate immune system responds rapidly and plays a key role in activating the adaptive immun...RNA viruses cause a multitude of human diseases,including several pandemic events in the past century.Upon viral invasion,the innate immune system responds rapidly and plays a key role in activating the adaptive immune system.In the innate immune system,the interactions between pathogen-associated molecular patterns and host pattern recognition receptors activate multiple signaling pathways in immune cells and induce the production of pro-inflammatory cytokines and interferons to elicit antiviral responses.Macrophages,dendritic cells,and natural killer cells are the principal innate immune components that exert antiviral activities.In this review,the current understanding of innate immunity contributing to the restriction of RNA viral infections was briefly summarized.Besides the main role of immune cells in combating viral infection,the intercellular transfer of pathogen and host-derived materials and their epigenetic and metabolic interactions associated with innate immunity was discussed.This knowledge provides an enhanced understanding of the innate immune response to RNA viral infections in general and aids in the preparation for the existing and next emerging viral infections.展开更多
Cells can adapt to environment and development by reconstructing their transcriptional networks to regulate diverse cellular processes without altering the underly- ing DNA sequences. These alterations, namely epige- ...Cells can adapt to environment and development by reconstructing their transcriptional networks to regulate diverse cellular processes without altering the underly- ing DNA sequences. These alterations, namely epige- netic changes, occur during cell division, differentiation and cell death. Numerous evidences demonstrate that epigenetic changes are governed by various types of determinants, including DNA methylation patterns, his- tone posttranslational modification signatures, histone variants, chromatin remodeling, and recently discovered chromosome conformation characteristics and non- coding RNAs (ncRNAs). Here, we highlight recent efforts on how the two latter epigenetic factors participate in the sophisticated transcriptional process and describe emerging techniques which permit us to uncover and gain insights into the fascinating genomic regulation.展开更多
基金supported by the Key Research and Development Program of Hubei Province(2020BBA032)the Wuhan Science and Technology Major Project “Development and application of polyploid rice”,the Open Research Fund of State Key Laboratory of Hybrid Rice(Hunan Hybrid Rice Research Center)(19KF06)the Youth Grant of Hubei University.
文摘Heterosis and polyploidy have an overwhelming influence on plant evolution.Recently,polyploid rice hybrids have been used to breed new rice varieties because they combine the advantages of both heterosis and polyploidy.In this study,we generated six rice lines:autotetraploid rice hybrids and their autotetraploid parents,diploid donors,and hybrids of the diploid donors.To investigate the molecular mechanism controlling the effects of both hybridization and polyploidization,we performed bisulfite and RNA sequencing on young panicles at the pollen meiosis stage to compare the DNA metabolomes and transcriptomes among the six rice lines.The hybrids lines were hypermethylated compared to their corresponding parents and the autotetraploid lines showed globally increased DNA methylation of their transposable elements compared to the diploid donors.The alteration in DNA methylation level corresponded to the differential gene expressions among the rice genotypes,suggesting that methylation changes induced by polyploidization and hybridization may affect gene expression.Groups of gene candidates were identified that may be associated with heterosis and polyploidy.Our results provide DNA information that can be used to investigate epigenetic modification during heterosis and polyploidy in rice.
基金supported by the National Natural Science Foundation of China (No.30870178)
文摘Previous studies have shown rapid and extensive genomic However, these studies are based on either a few pre-selected instability associated with early stages of allopolyploidization in wheat. genomic loci or genome-wide analysis of a single plant individual for a given cross combination, thus making the extent and generality of the changes uncertain. To further study the generality and characteristics of allopolyploidization-induced genomic instability in wheat, we investigated genetic and epigenetic changes from a genome-wide perspective (by using the AFLP and MSAP markers) in four sets of newly synthesized allotetraploid wheat lines with various genome constitutions, each containing three randomly chosen individual plants at the same generation. We document that although general chromosomal stability was characteristic of all four sets of allotetraploid wheat lines, genetic and epigenetic changes at the molecular level occurred in all these plants, with both kinds of changes classifiable into two distinct categories, i.e., stochastic and directed. The abundant type of genetic change is loss of parental bands while the prevalent cytosine methylation pattern alteration is hypermethylation at the CHG sites. Our results have extended previous studies regarding allopolyploidization-induced genomic dynamics in wheat by demonstrafing the generality of both genetic and epigenetic changes associated with multiple nascent allotetraploid wheat lines, and providing novel insights into the characteristics of the two kinds of induced genomic instabilities.
文摘In 2020,the International Agency for Research on Cancer and the World Health Organization's GLOBOCAN database ranked colorectal cancer(CRC)as the third most common cancer in the world.Most cases of CRC(>95%)are sporadic and develop from colorectal polyps that can progress to intramucosal carcinoma and CRC.Increasing evidence is accumulating that the gut microbiota can play a key role in the initiation and progression of CRC,as well as in the treatment of CRC,acting as an important metabolic and immunological regulator.Factors that may determine the microbiota role in CRC carcinogenesis include inflammation,changes in intestinal stem cell function,impact of bacterial metabolites on gut mucosa,accumulation of genetic mutations and other factors.In this review,I discuss the major mechanisms of the development of sporadic CRC,provide detailed characteristics of the bacteria that are most often associated with CRC,and analyze the role of the microbiome and microbial metabolites in inflammation initiation,activation of proliferative activity in intestinal epithelial and stem cells,and the development of genetic and epigenetic changes in CRC.I consider longterm studies in this direction to be very important,as they open up new opportunities for the treatment and prevention of CRC.
文摘Hepatitis C virus(HCV)chronic infection is associated with fibrosis progression,end-stage liver complications and HCC.Not surprisingly,HCV infection is a leading cause of liver-related morbidity and mortality worldwide.After sustained virological response(SVR),the risk of developing hepatocellular carcinoma is not completely eliminated in patients with established cirrhosis or with advanced fibrosis.Therefore,lifelong surveillance is currently recommended.This strategy is likely not universally cost-effective and harmless,considering that not all patients with advanced fibrosis have the same risk of developing HCC.Factors related to the severity of liver disease and its potential to improve after SVR,the molecular and epigenetic changes that occur during infection and other associated comorbidities might account for different risk levels and are likely essential for identifying patients who would benefit from screening programs after SVR.Efforts to develop predictive models and risk calculators,biomarkers and genetic panels and even deep learning models to estimate the individual risk of HCC have been made in the direct-acting antiviral agents era,when thousands of patients with advanced fibrosis and cirrhosis have reached SVR.These tools could help to identify patients with very low HCC risk in whom surveillance might not be justified.In this review,factors affecting the probability of HCC development after SVR,the benefits and risks of surveillance,suggested strategies to estimate individualized HCC risk and the current evidence to recommend lifelong surveillance are discussed.
文摘Nowadays,it is clear that adult stem cells,also called as tissue stem cells,play a central role to repair and maintain the tissue in which they reside by their selfrenewal ability and capacity of differentiating into distinct and specialized cells.As stem cells age,their renewal ability declines and their capacity to maintain organ homeostasis and regeneration is impaired.From a molecular perspective,these changes in stem cells properties can be due to several types of cell intrinsic injury and DNA aberrant alteration(i.e epigenomic profile)as well as changes in the tissue microenviroment,both into the niche and by systemic circulating factors.Strikingly,it has been suggested that aging-induced deterioration of stem cell functions may play a key role in the pathophysiology of the various agingassociated disorders.Therefore,understanding how resident stem cell age and affects near and distant tissues is fundamental.Here,we examine the current knowledge about aging mechanisms in several kinds of adult stem cells under physiological and pathological conditions and the principal aging-related changes in number,function and phenotype that determine the loss of tissue renewal properties.Furthermore,we examine the possible cell rejuvenation strategies.Stem cell rejuvenation may reverse the aging phenotype and the discovery of effective methods for inducing and differentiating pluripotent stem cells for cell replacement therapies could open up new possibilities for treating age-related diseases.
文摘RNA viruses cause a multitude of human diseases,including several pandemic events in the past century.Upon viral invasion,the innate immune system responds rapidly and plays a key role in activating the adaptive immune system.In the innate immune system,the interactions between pathogen-associated molecular patterns and host pattern recognition receptors activate multiple signaling pathways in immune cells and induce the production of pro-inflammatory cytokines and interferons to elicit antiviral responses.Macrophages,dendritic cells,and natural killer cells are the principal innate immune components that exert antiviral activities.In this review,the current understanding of innate immunity contributing to the restriction of RNA viral infections was briefly summarized.Besides the main role of immune cells in combating viral infection,the intercellular transfer of pathogen and host-derived materials and their epigenetic and metabolic interactions associated with innate immunity was discussed.This knowledge provides an enhanced understanding of the innate immune response to RNA viral infections in general and aids in the preparation for the existing and next emerging viral infections.
文摘Cells can adapt to environment and development by reconstructing their transcriptional networks to regulate diverse cellular processes without altering the underly- ing DNA sequences. These alterations, namely epige- netic changes, occur during cell division, differentiation and cell death. Numerous evidences demonstrate that epigenetic changes are governed by various types of determinants, including DNA methylation patterns, his- tone posttranslational modification signatures, histone variants, chromatin remodeling, and recently discovered chromosome conformation characteristics and non- coding RNAs (ncRNAs). Here, we highlight recent efforts on how the two latter epigenetic factors participate in the sophisticated transcriptional process and describe emerging techniques which permit us to uncover and gain insights into the fascinating genomic regulation.