In Arabidopsis, pericentromeric repeats, retroelements, and silenced rRNA genes are assembled into heterochromatin within nuclear structures known as chromocenters. The mechanisms governing higher-order heterochromati...In Arabidopsis, pericentromeric repeats, retroelements, and silenced rRNA genes are assembled into heterochromatin within nuclear structures known as chromocenters. The mechanisms governing higher-order heterochromatin organization are poorly understood but 24-nt small interfering RNAs （siRNAs） are known to play key roles in heterochromatin formation. Nuclear RNA polymerase IV （Pol IV）, RNA-DEPENDENT RNA POLYMERASE 2 （RDR2）, and DICER-LIKE 3 （DCL3） are required for biogenesis of 24-nt siRNAs that associate with ARGONAUTE 4 （AGO4）. Nuclear RNA polymerase V （Pol V） collaborates with DRD1 （DEFICIENT IN RNA-DEPENDENT DNA METHYLATION 1） to generate transcripts at heterochromatic loci that are hypothesized to bind to siRNA-AGO4 complexes and subsequently recruit the de-novo DNA methylation and/or histone modifying machinery. Here, we report that decondensation of the major pericentromeric repeats and depletion of the heterochromatic mark histone H3 lysine 9 dimethylation at chromocenters occurs specifically in pol V and drdl mutants. Disruption of pericentromeric repeats condensation is coincident with transcriptional reactivation of specific classes of pericentromeric 180-bp repeats. We further demonstrate that Pol V functions independently of Pol IV, RDR2, and DCL3-mediated siRNA production to affect interphase heterochromatin organization, possibly by involving RNAs that recruit structural or chromatin-modifying proteins.展开更多
RNA-directed DNA methylation(Rd DM) is a plant-specific de novo DNA methylation pathway,which has extensive cross-talk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMO...RNA-directed DNA methylation(Rd DM) is a plant-specific de novo DNA methylation pathway,which has extensive cross-talk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMOLOG 2(SHH2) is an H3 K9 me1 reader. Our structural studies reveal that H3 K9 me1 recognition is achieved by recognition of the methyl group via a classic aromatic cage and hydrogen-bonding and salt-bridge interactions with the free protons of the mono-methyllysine. The di-and tri-methylation states disrupt the polar interactions, decreasing the binding affinity. Our study reveals a monomethyllysine recognition mechanism which potentially links RdDM to H3 K9 me1 in maize.展开更多
Eukaryotic genomes encode thousands of non-coding RNAs （ncRNAs）, which play cru- cial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, esp...Eukaryotic genomes encode thousands of non-coding RNAs （ncRNAs）, which play cru- cial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially microRNAs （miRNAs） and long ncRNAs （lncRNAs）, have emerged as key regulatory molecules in plant stress responses. In this review, we have summa- rized the current progress on the understanding of plant miRNA and incRNA identification, characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA- and lncRNA-mediated plant stress tolerance.展开更多
Heat stress affects epigenetic gene silencing in Arabidopsis. To test for a mechanistic involvement of epige-netic regulation in heat-stress responses, we analyzed the heat tolerance of mutants defective in DNA methyl...Heat stress affects epigenetic gene silencing in Arabidopsis. To test for a mechanistic involvement of epige-netic regulation in heat-stress responses, we analyzed the heat tolerance of mutants defective in DNA methylation, his-tone modifications, chromatin-remodeling, or siRNA-based silencing pathways. Plants deficient in NRPD2, the common second-largest subunit of RNA polymerases IV and V, and in the Rpd3-type histone deacetylase HDA6 were hypersensi- tive to heat exposure. Microarray analysis demonstrated that NRPD2 and HDA6 have independent roles in transcriptional reprogramming in response to temperature stress. The misexpression of protein-coding genes in nrpd2 mutants recover-ing from heat correlated with defective epigenetic regulation of adjacent transposon remnants which involved the loss of control of heat-stress-induced read-through transcription. We provide evidence that the transcriptional response to temperature stress, at least partially, relies on the integrity of the RNA-dependent DNA methylation pathway.展开更多
DNA methylation is an important epigenetic marker for the suppression of transposable elements(TEs)and the regu-lation of plant immunity.However,little is known how RNA viruses counter defense such antiviral machinery...DNA methylation is an important epigenetic marker for the suppression of transposable elements(TEs)and the regu-lation of plant immunity.However,little is known how RNA viruses counter defense such antiviral machinery.In this study,the change of DNA methylation in turnip mosaic virus(TuMV)-infected cells was analyzed by whole genome bisulfite sequencing.Results showed that the total number of methylated sites of CHH and CHG increased in TuMV-infected cells,the majority of differentially methylated regions(DMRs)in the CHH and CHG contexts were associated with hypermethylation.Gene expression analysis showed that the expression of two methylases(DRM2 and CMT3)and three demethylases(ROS3,DML2,DML3)was significantly increased and decreased in TuMV-infected cells,respec-tively.Pathogenicity tests showed that the enhanced resistance to TuMV of the loss-of-function mutant of DRM2 is associated with unregulated expression of several defense-related genes.Finally,we found TuMV-encoded NIb,the viral RNA-dependent RNA polymerase,was able to induce the expression of DRM2.In conclusion,this study discov-ered that TuMV can modulate host DNA methylation by regulating the expression of DRM2 to promote virus infection.展开更多
Dynamic DNA methylation represses transposable elements(TEs)and regulates gene activity,playing a pivotal role in plant development.Although substantial progress has been made in understanding DNA methylation reprogra...Dynamic DNA methylation represses transposable elements(TEs)and regulates gene activity,playing a pivotal role in plant development.Although substantial progress has been made in understanding DNA methylation reprogramming during germline development in Arabidopsis thaliana,whether similar mechanisms exist in other dicot plants remains unclear.Here,we analyzed DNA methylation levels in meiocytes,microspores,and pollens of Brassica Rapa using whole-genome bisulfite sequencing(WGBS).Global DNA methylation analysis revealed similar CHH methylation reprogramming compared to Arabidopsis,while distinct patterns were observed in the dynamics of global CG and CHG methylation in B.rapa.Differentially methylated region(DMR)analysis identified specifically methylated loci in the male sex cells of B.Rapa with a stronger tendency to target genes,similar to observations in Arabidopsis.Additionally,we found that the activity and genomic targeting preference of the small RNA-directed DNA methylation(RdDM)were altered during B.Rapa male germline development.A subset of long terminal repeat(LTR)TEs were activated,possibly due to the dynamic regulation of DNA methylation during male sexual development in B.Rapa.These findings provided new insights into the evolution of epigenetic reprogramming mechanisms in plants.展开更多
文摘In Arabidopsis, pericentromeric repeats, retroelements, and silenced rRNA genes are assembled into heterochromatin within nuclear structures known as chromocenters. The mechanisms governing higher-order heterochromatin organization are poorly understood but 24-nt small interfering RNAs （siRNAs） are known to play key roles in heterochromatin formation. Nuclear RNA polymerase IV （Pol IV）, RNA-DEPENDENT RNA POLYMERASE 2 （RDR2）, and DICER-LIKE 3 （DCL3） are required for biogenesis of 24-nt siRNAs that associate with ARGONAUTE 4 （AGO4）. Nuclear RNA polymerase V （Pol V） collaborates with DRD1 （DEFICIENT IN RNA-DEPENDENT DNA METHYLATION 1） to generate transcripts at heterochromatic loci that are hypothesized to bind to siRNA-AGO4 complexes and subsequently recruit the de-novo DNA methylation and/or histone modifying machinery. Here, we report that decondensation of the major pericentromeric repeats and depletion of the heterochromatic mark histone H3 lysine 9 dimethylation at chromocenters occurs specifically in pol V and drdl mutants. Disruption of pericentromeric repeats condensation is coincident with transcriptional reactivation of specific classes of pericentromeric 180-bp repeats. We further demonstrate that Pol V functions independently of Pol IV, RDR2, and DCL3-mediated siRNA production to affect interphase heterochromatin organization, possibly by involving RNAs that recruit structural or chromatin-modifying proteins.
基金supported by National Natural Science Foundation of China(31770782)the Ministry of Science and Technology of China(2016YFA0503200)+1 种基金the Shenzhen Science and Technology Program(JCYJ20200109110403829 and KQTD20190929173906742)Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes(2019KSYS006)to J.D.
文摘RNA-directed DNA methylation(Rd DM) is a plant-specific de novo DNA methylation pathway,which has extensive cross-talk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMOLOG 2(SHH2) is an H3 K9 me1 reader. Our structural studies reveal that H3 K9 me1 recognition is achieved by recognition of the methyl group via a classic aromatic cage and hydrogen-bonding and salt-bridge interactions with the free protons of the mono-methyllysine. The di-and tri-methylation states disrupt the polar interactions, decreasing the binding affinity. Our study reveals a monomethyllysine recognition mechanism which potentially links RdDM to H3 K9 me1 in maize.
基金supported by the National Natural Science Foundation of China(Grant Nos.31611130033,31371328,and 31571366)Russian Foundation for Basic Research(Grant No.16-54-53064 and 15-04-05371)to OBD+4 种基金ICG SB RAS Budget Project(Grant No.0324-2016-0008)to YLOChina Scholarship Council&Deutscher Akademischer Austauschdienst(CSC&DAADProject-based Personnel Exchange ProgramGrant No.57136444)Science Technology Department of Zhejiang Province,China(Grant No.2015C32057)
文摘Eukaryotic genomes encode thousands of non-coding RNAs （ncRNAs）, which play cru- cial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially microRNAs （miRNAs） and long ncRNAs （lncRNAs）, have emerged as key regulatory molecules in plant stress responses. In this review, we have summa- rized the current progress on the understanding of plant miRNA and incRNA identification, characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA- and lncRNA-mediated plant stress tolerance.
文摘Heat stress affects epigenetic gene silencing in Arabidopsis. To test for a mechanistic involvement of epige-netic regulation in heat-stress responses, we analyzed the heat tolerance of mutants defective in DNA methylation, his-tone modifications, chromatin-remodeling, or siRNA-based silencing pathways. Plants deficient in NRPD2, the common second-largest subunit of RNA polymerases IV and V, and in the Rpd3-type histone deacetylase HDA6 were hypersensi- tive to heat exposure. Microarray analysis demonstrated that NRPD2 and HDA6 have independent roles in transcriptional reprogramming in response to temperature stress. The misexpression of protein-coding genes in nrpd2 mutants recover-ing from heat correlated with defective epigenetic regulation of adjacent transposon remnants which involved the loss of control of heat-stress-induced read-through transcription. We provide evidence that the transcriptional response to temperature stress, at least partially, relies on the integrity of the RNA-dependent DNA methylation pathway.
基金supported by the National Natural Science Foundation of China(32022071,31860491)the Natural Science Foundation of Heilongjiang Province(Grant No.LH2019C027)+1 种基金the Academic Backbone Projects of Northeast Agricultural University(18XG04)the project of China National Tobacco Corporation(110202002010-JY-13).
文摘DNA methylation is an important epigenetic marker for the suppression of transposable elements(TEs)and the regu-lation of plant immunity.However,little is known how RNA viruses counter defense such antiviral machinery.In this study,the change of DNA methylation in turnip mosaic virus(TuMV)-infected cells was analyzed by whole genome bisulfite sequencing.Results showed that the total number of methylated sites of CHH and CHG increased in TuMV-infected cells,the majority of differentially methylated regions(DMRs)in the CHH and CHG contexts were associated with hypermethylation.Gene expression analysis showed that the expression of two methylases(DRM2 and CMT3)and three demethylases(ROS3,DML2,DML3)was significantly increased and decreased in TuMV-infected cells,respec-tively.Pathogenicity tests showed that the enhanced resistance to TuMV of the loss-of-function mutant of DRM2 is associated with unregulated expression of several defense-related genes.Finally,we found TuMV-encoded NIb,the viral RNA-dependent RNA polymerase,was able to induce the expression of DRM2.In conclusion,this study discov-ered that TuMV can modulate host DNA methylation by regulating the expression of DRM2 to promote virus infection.
基金support of National Natural Science Foundation of China(Grant No.32070608).
文摘Dynamic DNA methylation represses transposable elements(TEs)and regulates gene activity,playing a pivotal role in plant development.Although substantial progress has been made in understanding DNA methylation reprogramming during germline development in Arabidopsis thaliana,whether similar mechanisms exist in other dicot plants remains unclear.Here,we analyzed DNA methylation levels in meiocytes,microspores,and pollens of Brassica Rapa using whole-genome bisulfite sequencing(WGBS).Global DNA methylation analysis revealed similar CHH methylation reprogramming compared to Arabidopsis,while distinct patterns were observed in the dynamics of global CG and CHG methylation in B.rapa.Differentially methylated region(DMR)analysis identified specifically methylated loci in the male sex cells of B.Rapa with a stronger tendency to target genes,similar to observations in Arabidopsis.Additionally,we found that the activity and genomic targeting preference of the small RNA-directed DNA methylation(RdDM)were altered during B.Rapa male germline development.A subset of long terminal repeat(LTR)TEs were activated,possibly due to the dynamic regulation of DNA methylation during male sexual development in B.Rapa.These findings provided new insights into the evolution of epigenetic reprogramming mechanisms in plants.
