DNA methylation is a key chromatin modification in plant genomes that is meiotically and mitotically her- itable, and at times is associated with gene expression and morphological variation. Benefiting from the increa...DNA methylation is a key chromatin modification in plant genomes that is meiotically and mitotically her- itable, and at times is associated with gene expression and morphological variation. Benefiting from the increased availability of high-quality reference genome assemblies and methods to profile single-base res- olution DNA methylation states, DNA methylomes for many crop species are available. These efforts are making it possible to begin answering crucial questions, including understanding the role of DNA methyl- ation in developmental processes, its role in crop species evolution, and whether DNA methylation is dynamically altered and heritable in response to changes in the environment. These genome-wide maps provide evidence for the existence of silent epialleles in plant genomes which, once identified, can be tar- geted for reactivation leading to phenotypic variation.展开更多
Whole-genome bisulfite sequencing(WGBS)allows single-base resolution and genome-wide profiling of DNA methylation in plants and animals.This technology provides a powerful tool to identify genes that are potentially c...Whole-genome bisulfite sequencing(WGBS)allows single-base resolution and genome-wide profiling of DNA methylation in plants and animals.This technology provides a powerful tool to identify genes that are potentially controlled by dynamic changes of DNA methylation and demethylation.However,naturally occurring epimutants are rare and genes under epigenetic regulation as well as their biological relevances are often difficult to define.In tomato,fruit development and ripening are a complex process that involves epigenetic control.We have taken the advantage of the tomato epimutant Colourless non-ripening(Cnr)and performed comparative mining of the WGBS datasets for the Cnr and Sl CMT3-silenced Cnr fruits.We compared DNA methylation profiles for the promoter sequences of approximately 5,000 bp immediately upstream of the coding region of a list of20 genes.Differentially methylated regions were found for some of these genes.Virus-induced gene silencing(VIGS)of differentially methylated gene Sl DET1 or Sl PDS resulted in unusual brown pigmentation in Cnr fruits.These results suggest that comparative WGBS coupled with VIGS can be used to identify genes that may contribute to the colourless unripe phenotype of fruit in the Cnr epimutant.展开更多
Dominance relationships between males and their associated traits are usually heritable and have implications for sexual selection in animals.In particular,social dominance and its related male pheromones are heritabl...Dominance relationships between males and their associated traits are usually heritable and have implications for sexual selection in animals.In particular,social dominance and its related male pheromones are heritable in inbred mice;thus,we wondered whether epigenetic changes due to altered levels of DNA methylation determine inheritance.Here,we used C57BL/6 male mice to establish a social dominance-subordination relationship through chronic dyadic encounters,and this relationship and pheromone covariation occurred in their offspring,indicative of heritability.Through transcriptome sequencing and whole-genome DNA methylation profiling of the sperm of both generations,we found that differential methylation of many genes was induced by social dominance-subordination in sires and could be passed on to the offspring.These methylated genes were mainly related to growth and development processes,neurodevelopment,and cellular transportation.The expression of the genes with similar functions in whole-genome methylation/bisulfite sequencing was also differentiated by social dominance-subordination,as revealed by RNA-seq.In particular,the gene Dennd1a,which regulates neural signaling,was differentially methylated and expressed in the sperm and medial prefrontal cortex in paired males before and after dominance-subordination establishment,suggesting the potential epigenetic control and inheritance of social dominance-related aggression.We suggest that social dominance might be passed on to male offspring through sperm DNA methylation and that the differences could potentially affect male competition in offspring by affecting the development of thenervous system.展开更多
Caste differentiation in social hymenopterans is an intriguing example of phenotypic plasticity. However, the co-ordination among gene regulatory factors to mediate caste differentiation remains inconclusive. In this ...Caste differentiation in social hymenopterans is an intriguing example of phenotypic plasticity. However, the co-ordination among gene regulatory factors to mediate caste differentiation remains inconclusive. In this study, we determined the role of gene regulation and related epigenetic processes in pre-imaginal caste differentiation in the primitively eusocial bumblebee Bombus terrestris. By combining RNA-Seq data from Illumina and Pac Bio and accurately quantifying methylation at whole-genomic base pair resolution, we found that queens, workers, and drones mainly differentiate in gene expression but not in alternative splicing and DNA methylation. Gynes are the most distinct with the lowest global level of whole-genomic methylation and with the largest number of caste-specific transcripts and alternative splicing events. By contrast, workers exhibit few uniquely expressed or alternatively spliced genes. Moreover, several genes involved in hormone and neurotransmitter metabolism are related to caste differentiation, whereas several neuropeptides are linked with sex differentiation. Despite little genome-wide association among differential gene expression, splicing, and differential DNA methylation, the overlapped gene ontology(GO) terms point to nutrition-related activity. Therefore, variations in gene regulation correlate with the behavioral differences among castes and highlight the specialization of toolkit genes in bumblebee gynes at the beginning of the adult stage.展开更多
文摘DNA methylation is a key chromatin modification in plant genomes that is meiotically and mitotically her- itable, and at times is associated with gene expression and morphological variation. Benefiting from the increased availability of high-quality reference genome assemblies and methods to profile single-base res- olution DNA methylation states, DNA methylomes for many crop species are available. These efforts are making it possible to begin answering crucial questions, including understanding the role of DNA methyl- ation in developmental processes, its role in crop species evolution, and whether DNA methylation is dynamically altered and heritable in response to changes in the environment. These genome-wide maps provide evidence for the existence of silent epialleles in plant genomes which, once identified, can be tar- geted for reactivation leading to phenotypic variation.
基金supported by Ministry of Agriculture of the People’s Republic of Chinathe National Transgenic Program of China (2016ZX08009001-004 to Yiguo Hong)+4 种基金National Natural Science Foundation of China (31370180 to Yiguo Hong, 31601765 to Weiwei Chen)Hangzhou Normal University Pandeng Program (201108 to Yiguo Hong)the Hangzhou City Government Innovative Program for Science Excellence (20131028 to Yiguo Hong)Zhejiang Provincial Natural Science Foundation (LY14C010005 to Nongnong Shi)the UK Biotechnology and Biological Sciences Research Council (BBS/E/H/00YH0271 to Yiguo Hong)
文摘Whole-genome bisulfite sequencing(WGBS)allows single-base resolution and genome-wide profiling of DNA methylation in plants and animals.This technology provides a powerful tool to identify genes that are potentially controlled by dynamic changes of DNA methylation and demethylation.However,naturally occurring epimutants are rare and genes under epigenetic regulation as well as their biological relevances are often difficult to define.In tomato,fruit development and ripening are a complex process that involves epigenetic control.We have taken the advantage of the tomato epimutant Colourless non-ripening(Cnr)and performed comparative mining of the WGBS datasets for the Cnr and Sl CMT3-silenced Cnr fruits.We compared DNA methylation profiles for the promoter sequences of approximately 5,000 bp immediately upstream of the coding region of a list of20 genes.Differentially methylated regions were found for some of these genes.Virus-induced gene silencing(VIGS)of differentially methylated gene Sl DET1 or Sl PDS resulted in unusual brown pigmentation in Cnr fruits.These results suggest that comparative WGBS coupled with VIGS can be used to identify genes that may contribute to the colourless unripe phenotype of fruit in the Cnr epimutant.
基金supported by the National Natural Science Foundation of China(grant numbers 31872227 and 32070451)the Strategic Priority Research Program of the Chinese Academy of Sciences(grant no.XDPB16).
文摘Dominance relationships between males and their associated traits are usually heritable and have implications for sexual selection in animals.In particular,social dominance and its related male pheromones are heritable in inbred mice;thus,we wondered whether epigenetic changes due to altered levels of DNA methylation determine inheritance.Here,we used C57BL/6 male mice to establish a social dominance-subordination relationship through chronic dyadic encounters,and this relationship and pheromone covariation occurred in their offspring,indicative of heritability.Through transcriptome sequencing and whole-genome DNA methylation profiling of the sperm of both generations,we found that differential methylation of many genes was induced by social dominance-subordination in sires and could be passed on to the offspring.These methylated genes were mainly related to growth and development processes,neurodevelopment,and cellular transportation.The expression of the genes with similar functions in whole-genome methylation/bisulfite sequencing was also differentiated by social dominance-subordination,as revealed by RNA-seq.In particular,the gene Dennd1a,which regulates neural signaling,was differentially methylated and expressed in the sperm and medial prefrontal cortex in paired males before and after dominance-subordination establishment,suggesting the potential epigenetic control and inheritance of social dominance-related aggression.We suggest that social dominance might be passed on to male offspring through sperm DNA methylation and that the differences could potentially affect male competition in offspring by affecting the development of thenervous system.
基金supported by the National Natural Science Foundation of China (31930012, 31920103004, and 31772531)the Science and Technology Service Network Initiative of the Chinese Academy of Sciences (KFJ-STS-ZDTP-073)+1 种基金the Joint NSFC-ISF Research Grant (3201101042)the State Key Laboratory of Integrated Management of Pest Insects and Rodents (Y852981203)。
文摘Caste differentiation in social hymenopterans is an intriguing example of phenotypic plasticity. However, the co-ordination among gene regulatory factors to mediate caste differentiation remains inconclusive. In this study, we determined the role of gene regulation and related epigenetic processes in pre-imaginal caste differentiation in the primitively eusocial bumblebee Bombus terrestris. By combining RNA-Seq data from Illumina and Pac Bio and accurately quantifying methylation at whole-genomic base pair resolution, we found that queens, workers, and drones mainly differentiate in gene expression but not in alternative splicing and DNA methylation. Gynes are the most distinct with the lowest global level of whole-genomic methylation and with the largest number of caste-specific transcripts and alternative splicing events. By contrast, workers exhibit few uniquely expressed or alternatively spliced genes. Moreover, several genes involved in hormone and neurotransmitter metabolism are related to caste differentiation, whereas several neuropeptides are linked with sex differentiation. Despite little genome-wide association among differential gene expression, splicing, and differential DNA methylation, the overlapped gene ontology(GO) terms point to nutrition-related activity. Therefore, variations in gene regulation correlate with the behavioral differences among castes and highlight the specialization of toolkit genes in bumblebee gynes at the beginning of the adult stage.
