DNA methylation and demethylation activities are coordinated to maintain DNA methylation patterns.However,the interplay between them remains to be explored.In this study,we found that loss of DNA demethylase in maize ...DNA methylation and demethylation activities are coordinated to maintain DNA methylation patterns.However,the interplay between them remains to be explored.In this study,we found that loss of DNA demethylase in maize results in a significant decrease in CHH methylation,a hallmark of RNA-directed DNA methylation(RdDM).Further analyses suggested that this is caused by reduced expression in the DNA demethylase mutant of three CLASSY(CLSY)genes,which encode chromatin remodelers controlling small RNA production.Series of molecular assays confirm that the expression of three maize CLSY genes is sensitive to the DNA methylation levels at their promoter regions,which are regulated by both the DNA demethylase and the RdDM pathway.Moreover,we revealed that Arabidopsis DNA demethylase mutants also show decreased CHH methylation and reduced expression of CLSY1,one of four CLSY genes in Arabidopsis.Similar to the observations in maize,the expression of CLSY1 is associated with DNA methylation levels of its promoter that is targeted by both DNA demethylase and RdDM pathways.Taken together,these results suggest a conserved interplay between DNA demethylation and RdDM pathways,revealing a mechanism to maintain the homeostasis of DNA methylation levels across plants.展开更多
Gene expression variation is a key component underlying phenotypic variation and heterosis. Transcriptome profiling was performed on 23 different tissues or developmental stages of two maize inbreds, B73 and Mo17, as ...Gene expression variation is a key component underlying phenotypic variation and heterosis. Transcriptome profiling was performed on 23 different tissues or developmental stages of two maize inbreds, B73 and Mo17, as well as their hybrid. The obtained large-scale datasets provided opportunities to monitor the developmental dynamics of differential expression, additivity for gene expression, and regulatory variation. The transcriptome can be divided into .30 000 genes that are expressed in at least one tissue of one in bred and an additional ~10 000 “silent” genes that are not expressed in any tissue of any genotype, 90% of which are non-syntenic relative to other grasses. Many (.74%) of the expressed genes exhibit differential expression in at least one tissue. However, the majority of genes with differential expression do not exhibit consistent differential expression in different tissues. These genes often exhibit tissue-specific differential expression with equivalent expression in other tissues, and in many cases they switch the directionality of differential expression in different tissues. This suggests widespread variation for tissue-specific regulation of gene expression between the two maize inbreds B73 and Mo17. Nearly 5000 genes are expressed in only one parent in at least one tissue (single parent expression) and 97% of these genes are expressed at mid-parent levels or higher in the hybrid, providing extensive opportunities for hybrid complementation in heterosis. In general, additive expression patterns are much more common than non-additive patterns, and this trend is more pronounced for genes with strong differential expression or single pare nt expressi on. There is relatively little evidence for non-additive expression patterns that are maintained in multiple tissues. The analysis of allele-specific expression allowed classification of cis. and trans-regulatory variation. Genes with c/s-regulatory variation often exhibit additive expression and tend to have more consistent regulatory variation throughout development. In contrast, genes with trans-reguiatory variation are enriched for non-additive patterns and often show tissue-specific differential expression. Taken together, this study provides a deeper understatiding of regulatory variation and the degree of additive gene expression throughout maize development. The dynamic nature of differential expression, additivity, and regulatory variation imply abundant variability for tissue-specific regulatory mechanisms and suggest that connections between transcriptome and phenome will require expression data from multiple tissues.展开更多
DNA methylation is a chromatin modification that is often associated with the exciti ng and sometimes unpredictable patter ns of inheritanee that can unfold with epigenetic phenomena. The stability and heritability of...DNA methylation is a chromatin modification that is often associated with the exciti ng and sometimes unpredictable patter ns of inheritanee that can unfold with epigenetic phenomena. The stability and heritability of DNA methylati on patter ns perhaps allow us to utilize DNA methylation profiles to distil the suite of potentially functional elements in large crop genomes. Here, we discuss the potential and possible ways to use the absence of DNA methylation to identify potential regulatory regions within intergenic sequences and the presence of DNA methylation to identify pseudogenes.展开更多
基金supported by the Foundation for Innovative Research Groups of the National Natural Science Foundation of China(32321005)the 111 Project Crop Genomics and Molecular Breeding(B20051)+1 种基金the Outstanding Youth Team Cultivation Project of Central Universities(2662023PY007)the Postdoctoral Fellowship Program of CPSF undergrantnumberGZB20240254.
文摘DNA methylation and demethylation activities are coordinated to maintain DNA methylation patterns.However,the interplay between them remains to be explored.In this study,we found that loss of DNA demethylase in maize results in a significant decrease in CHH methylation,a hallmark of RNA-directed DNA methylation(RdDM).Further analyses suggested that this is caused by reduced expression in the DNA demethylase mutant of three CLASSY(CLSY)genes,which encode chromatin remodelers controlling small RNA production.Series of molecular assays confirm that the expression of three maize CLSY genes is sensitive to the DNA methylation levels at their promoter regions,which are regulated by both the DNA demethylase and the RdDM pathway.Moreover,we revealed that Arabidopsis DNA demethylase mutants also show decreased CHH methylation and reduced expression of CLSY1,one of four CLSY genes in Arabidopsis.Similar to the observations in maize,the expression of CLSY1 is associated with DNA methylation levels of its promoter that is targeted by both DNA demethylase and RdDM pathways.Taken together,these results suggest a conserved interplay between DNA demethylation and RdDM pathways,revealing a mechanism to maintain the homeostasis of DNA methylation levels across plants.
基金a grant from the National Science Foundation (#1546899) to S.P.B and N.M.S.
文摘Gene expression variation is a key component underlying phenotypic variation and heterosis. Transcriptome profiling was performed on 23 different tissues or developmental stages of two maize inbreds, B73 and Mo17, as well as their hybrid. The obtained large-scale datasets provided opportunities to monitor the developmental dynamics of differential expression, additivity for gene expression, and regulatory variation. The transcriptome can be divided into .30 000 genes that are expressed in at least one tissue of one in bred and an additional ~10 000 “silent” genes that are not expressed in any tissue of any genotype, 90% of which are non-syntenic relative to other grasses. Many (.74%) of the expressed genes exhibit differential expression in at least one tissue. However, the majority of genes with differential expression do not exhibit consistent differential expression in different tissues. These genes often exhibit tissue-specific differential expression with equivalent expression in other tissues, and in many cases they switch the directionality of differential expression in different tissues. This suggests widespread variation for tissue-specific regulation of gene expression between the two maize inbreds B73 and Mo17. Nearly 5000 genes are expressed in only one parent in at least one tissue (single parent expression) and 97% of these genes are expressed at mid-parent levels or higher in the hybrid, providing extensive opportunities for hybrid complementation in heterosis. In general, additive expression patterns are much more common than non-additive patterns, and this trend is more pronounced for genes with strong differential expression or single pare nt expressi on. There is relatively little evidence for non-additive expression patterns that are maintained in multiple tissues. The analysis of allele-specific expression allowed classification of cis. and trans-regulatory variation. Genes with c/s-regulatory variation often exhibit additive expression and tend to have more consistent regulatory variation throughout development. In contrast, genes with trans-reguiatory variation are enriched for non-additive patterns and often show tissue-specific differential expression. Taken together, this study provides a deeper understatiding of regulatory variation and the degree of additive gene expression throughout maize development. The dynamic nature of differential expression, additivity, and regulatory variation imply abundant variability for tissue-specific regulatory mechanisms and suggest that connections between transcriptome and phenome will require expression data from multiple tissues.
文摘DNA methylation is a chromatin modification that is often associated with the exciti ng and sometimes unpredictable patter ns of inheritanee that can unfold with epigenetic phenomena. The stability and heritability of DNA methylati on patter ns perhaps allow us to utilize DNA methylation profiles to distil the suite of potentially functional elements in large crop genomes. Here, we discuss the potential and possible ways to use the absence of DNA methylation to identify potential regulatory regions within intergenic sequences and the presence of DNA methylation to identify pseudogenes.
