Dimethylation of histone H3 lysine 9 （H3K9me2） is an important epigenetic mark associated with transcription repression. Here, we identified PHF8, a JmjC-domain-containing protein, as a histone demethylase specific ...Dimethylation of histone H3 lysine 9 （H3K9me2） is an important epigenetic mark associated with transcription repression. Here, we identified PHF8, a JmjC-domain-containing protein, as a histone demethylase specific for this repressing mark. Recombinant full-length wild type protein could remove methylation from H3K9me2, but mutation of a conserved histidine to alanine H247A abolished the demethylase activity. Overexpressed exogenous PHF8 was colocalized with B23 staining. Endogenous PHF8 was also colocalized with B23 and fibrillarin, two well-established nucleolus proteins, suggesting that PHF8 is localized in the nucleolus and may regulate rRNA transcription. Indeed, PHF8 bound to the promoter region of the rDNA gene. Knockdown of PHF8 reduced the expression of rRNA, and overexpression of the gene resulted in upregulation of rRNA transcript. Concomitantly, H3K9me2 level was elevated in the promoter region of the rDNA gene in PHF8 knockdown cells and reduced significantly when the wild type but not the catalytically inactive H247A mutant PHF8 was overexpressed. Thus, our study identified a histone demethylase for H3K9me2 that regulates rRNA transcription.展开更多
Maintaining genomic integrity and stability is particularly important for stem cells,which are at the top of the cell lineage origin.Here,we discovered that the plant-specific histone methyltransferase SUVR2 maintains...Maintaining genomic integrity and stability is particularly important for stem cells,which are at the top of the cell lineage origin.Here,we discovered that the plant-specific histone methyltransferase SUVR2 maintains the genome integrity of the root tip stem cells through chromatin remodeling and liquid-liquid phase separation(LLPS)when facing DNA double-strand breaks(DSBs).The histone methyltransferase SUVR2(MtSUVR2)has histone methyltransferase activity and catalyzes the conversion of histone H3 lysine 9 monomethylation(H3K9me1)to H3K9me2/3 in vitro and in Medicago truncatula.Under DNA damage,the proportion of heterochromatin decreased and the level of DSB damage marker y-H2AX increased in suvr2 mutants,indicating that MtSUVR2 promotes the compaction of the chromatin structure through H3K9 methylation modification to protect DNA from damage.Interestingly,MtSUVR2 was induced by DSBs to phase separate and form droplets to localize at the damage sites,and this was confirmed by immunofluorescence and fluorescence recovery after photobleaching experiments.The IDR1 and lowcomplexity domain regions of MtSUVR2 determined its phase separation in the nucleus,whereas the IDR2 region determined the interaction with the homologous recombinase MtRAD51.Furthermore,we found that MtSUVR2 drove the phase separation of MtRAD51 to form"DNA repair bodies,"which could enhance the stability of MtRAD51 proteins to facilitate error-free homologous recombination repair of stem cells.Taken together,our study reveals that chromatin remodeling-associated proteins participate in DNA repair through LLPS.展开更多
H3K9me2 and H3K27me2 are important epigenetic marks associated with transcription repression, while H3K4me3 is associated with transcription activation. It has been shown that active and repressive histone methylation...H3K9me2 and H3K27me2 are important epigenetic marks associated with transcription repression, while H3K4me3 is associated with transcription activation. It has been shown that active and repressive histone methylations distribute in a mutually exclusive manner, but the underlying mechanism was poorly understood. Here we identified ceKDM7A, a PHD （plant homeodomain）- and JmjC domain-containing protein, as a histone demethylase specific for H3K9me2 and H3K27me2. We further demonstrated that the PHD domain of ceKDM7A bound H3K4me3 and H3K4me3 co-localized with ceKDM7A at the genome-wide level. Disruption of the PHD domain binding to H3K4me3 reduced the demethylase activity in vivo, and loss of ceKDM7A reduced the expression of its associated target genes. These results indicate that ceKDM7A is recruited to the promoter to demethylate H3K9me2 and H3K27me2 and activate gene expression through the binding of the PHD domain to H3K4me3. Thus, our study identifies a dual-specificity histone demethylase and provides novel insights into the regulation of histone methylation.展开更多
DNA methylation,a conserved epigenetic mark,is critical for tuning temporal and spatial gene expression.The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1(ROS1)initiates active DNA demethylation a...DNA methylation,a conserved epigenetic mark,is critical for tuning temporal and spatial gene expression.The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1(ROS1)initiates active DNA demethylation and is required to prevent DNA hypermethylation at thousands of genomic loci.However,how ROS1 is recruited to specific loci is not well understood.Here,we report the discovery of Arabidopsis AGENET Domain Containing Protein 3(AGDP3)as a cellular factor that is required to prevent gene silencing and DNA hypermethylation.AGDP3 binds to H3K9me2 marks in its target DNA via its AGD12 cassette.Analysis of the crystal structure of the AGD12 cassette of AGDP3 in complex with an H3K9me2 peptide revealed that dimethylated H3 K9 and unmodified H3 K4 are specifically anchored into two different surface pockets.A histidine residue located in the methyllysine binding aromatic cage provides AGDP3 with pH-dependent H3K9me2 binding capacity.Our results uncover a molecular mechanism for the regulation of DNA demethylation by the gene silencing mark H3K9me2.展开更多
Serving as a host factor for human immunodeficiency virus(HIV)integration,LEDGF/p75 has been under extensive study as a potential target for therapy.However,as a highly conserved protein,its physiological function rem...Serving as a host factor for human immunodeficiency virus(HIV)integration,LEDGF/p75 has been under extensive study as a potential target for therapy.However,as a highly conserved protein,its physiological function remains to be thoroughly elucidated.Here,we characterize the molecular function of dP75,the Drosophila homolog of LEDGF/p75,during oogenesis.dP75 binds to transcriptionally active chromatin with its PWWP domain.The C-terminus integrase-binding domain-containing region of dP75 physically interacts with the histone kinase Jil-1 and stabilizes it in vivo.Together with Jil-1,dP75 prevents the spreading of the heterochromatin mark-H3 K9 me2-onto genes required for oogenesis and piRNA production.Without dP75,ectopical silencing of these genes disrupts oogenesis,activates transposons,and causes animal sterility.We propose that dP75,the homolog of an HIV host factor in Drosophila,partners with and stabilizes Jil-1 to ensure gene expression during oogenesis by preventing ectopic heterochromatin spreading.展开更多
In the nucleus, chromatin is folded into hierarchical architecture that is tightly linked to various nuclear functions. However, the underlying molecular mechanisms that confer these architectures remain incompletely ...In the nucleus, chromatin is folded into hierarchical architecture that is tightly linked to various nuclear functions. However, the underlying molecular mechanisms that confer these architectures remain incompletely understood. Here, we investigated the functional roles of H3 lysine 9 dimethylation(H3 K9 me2), one of the abundant histone modifications, in three-dimensional(3 D)genome organization. Unlike in mouse embryonic stem cells, inhibition of methyltransferases G9 a and GLP in differentiated cells eliminated H3 K9 me2 predominantly at A-type(active) genomic compartments, and the level of residual H3 K9 me2 modifications was strongly associated with B-type(inactive) genomic compartments. Furthermore, chemical inhibition of G9 a/GLP in mouse hepatocytes led to decreased chromatin-nuclear lamina interactions mainly at G9 a/GLP-sensitive regions, increased degree of genomic compartmentalization, and up-regulation of hundreds of genes that were associated with alterations of the 3 D chromatin. Collectively, our data demonstrated essential roles of H3 K9 me2 in 3 D genome organization.展开更多
Cells need to appropriately balance transcriptional stability and adaptability in order to maintain their identities while responding robustly to various stimuli. Eukaryotic cells use an elegant "epigenetic"...Cells need to appropriately balance transcriptional stability and adaptability in order to maintain their identities while responding robustly to various stimuli. Eukaryotic cells use an elegant "epigenetic" system to achieve this functionality. "Epigenetics" is referred to as heritable information beyond the DNA sequence, including histone and DNA modifications, nc RNAs and other chromatin-related components. Here, we review the mechanisms of the epigenetic inheritance of a repressive chromatin state,with an emphasis on recent progress in the field. We emphasize that(i) epigenetic information is inherited in a relatively stable but imprecise fashion;(ii) multiple cis and trans factors are involved in the maintenance of epigenetic information during mitosis; and(iii) the maintenance of a repressive epigenetic state requires both recruitment and self-reinforcement mechanisms.These mechanisms crosstalk with each other and form interconnected feedback loops to shape a stable epigenetic system while maintaining certain degrees of flexibility.展开更多
基金Acknowledgments We thank the cell biology core facility for confocal study. The PHF8 antibody was kindly provided by Dr Jiemin Wong （East China Normal University）. This work was supported by the National Basic Research Program of China （2007CB947900, 2010CB529705, 2007CB947100）, the Chinese Academy of Sci- ences （KSCX2-YW-R-04, KSCX2-YW-R-I 11）, the National Natural Science Foundation of China （30870538, 90919026）, Postdoctoral fellowship （20090460670）, and the Council of Shanghai Municipal Government for Science and Technology.
文摘Dimethylation of histone H3 lysine 9 （H3K9me2） is an important epigenetic mark associated with transcription repression. Here, we identified PHF8, a JmjC-domain-containing protein, as a histone demethylase specific for this repressing mark. Recombinant full-length wild type protein could remove methylation from H3K9me2, but mutation of a conserved histidine to alanine H247A abolished the demethylase activity. Overexpressed exogenous PHF8 was colocalized with B23 staining. Endogenous PHF8 was also colocalized with B23 and fibrillarin, two well-established nucleolus proteins, suggesting that PHF8 is localized in the nucleolus and may regulate rRNA transcription. Indeed, PHF8 bound to the promoter region of the rDNA gene. Knockdown of PHF8 reduced the expression of rRNA, and overexpression of the gene resulted in upregulation of rRNA transcript. Concomitantly, H3K9me2 level was elevated in the promoter region of the rDNA gene in PHF8 knockdown cells and reduced significantly when the wild type but not the catalytically inactive H247A mutant PHF8 was overexpressed. Thus, our study identified a histone demethylase for H3K9me2 that regulates rRNA transcription.
基金the Key Projects in Science and Technology of Inner Mongolia(2021ZD0031)the Opening Fund of the Key Laboratory of Forage and Endemic Crop Biology,the Ministry of Education(FECBOF2021001)+1 种基金the National Natural Science Foundation of China(NFSC32070272)for supporting this work.
文摘Maintaining genomic integrity and stability is particularly important for stem cells,which are at the top of the cell lineage origin.Here,we discovered that the plant-specific histone methyltransferase SUVR2 maintains the genome integrity of the root tip stem cells through chromatin remodeling and liquid-liquid phase separation(LLPS)when facing DNA double-strand breaks(DSBs).The histone methyltransferase SUVR2(MtSUVR2)has histone methyltransferase activity and catalyzes the conversion of histone H3 lysine 9 monomethylation(H3K9me1)to H3K9me2/3 in vitro and in Medicago truncatula.Under DNA damage,the proportion of heterochromatin decreased and the level of DSB damage marker y-H2AX increased in suvr2 mutants,indicating that MtSUVR2 promotes the compaction of the chromatin structure through H3K9 methylation modification to protect DNA from damage.Interestingly,MtSUVR2 was induced by DSBs to phase separate and form droplets to localize at the damage sites,and this was confirmed by immunofluorescence and fluorescence recovery after photobleaching experiments.The IDR1 and lowcomplexity domain regions of MtSUVR2 determined its phase separation in the nucleus,whereas the IDR2 region determined the interaction with the homologous recombinase MtRAD51.Furthermore,we found that MtSUVR2 drove the phase separation of MtRAD51 to form"DNA repair bodies,"which could enhance the stability of MtRAD51 proteins to facilitate error-free homologous recombination repair of stem cells.Taken together,our study reveals that chromatin remodeling-associated proteins participate in DNA repair through LLPS.
文摘H3K9me2 and H3K27me2 are important epigenetic marks associated with transcription repression, while H3K4me3 is associated with transcription activation. It has been shown that active and repressive histone methylations distribute in a mutually exclusive manner, but the underlying mechanism was poorly understood. Here we identified ceKDM7A, a PHD （plant homeodomain）- and JmjC domain-containing protein, as a histone demethylase specific for H3K9me2 and H3K27me2. We further demonstrated that the PHD domain of ceKDM7A bound H3K4me3 and H3K4me3 co-localized with ceKDM7A at the genome-wide level. Disruption of the PHD domain binding to H3K4me3 reduced the demethylase activity in vivo, and loss of ceKDM7A reduced the expression of its associated target genes. These results indicate that ceKDM7A is recruited to the promoter to demethylate H3K9me2 and H3K27me2 and activate gene expression through the binding of the PHD domain to H3K4me3. Thus, our study identifies a dual-specificity histone demethylase and provides novel insights into the regulation of histone methylation.
基金the Chinese Academy of Sciences and the National Natural Science Foundation of China(31970580)to M.L.the National Key R&D Program(2016YFA0503200)+1 种基金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DNA methylation,a conserved epigenetic mark,is critical for tuning temporal and spatial gene expression.The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1(ROS1)initiates active DNA demethylation and is required to prevent DNA hypermethylation at thousands of genomic loci.However,how ROS1 is recruited to specific loci is not well understood.Here,we report the discovery of Arabidopsis AGENET Domain Containing Protein 3(AGDP3)as a cellular factor that is required to prevent gene silencing and DNA hypermethylation.AGDP3 binds to H3K9me2 marks in its target DNA via its AGD12 cassette.Analysis of the crystal structure of the AGD12 cassette of AGDP3 in complex with an H3K9me2 peptide revealed that dimethylated H3 K9 and unmodified H3 K4 are specifically anchored into two different surface pockets.A histidine residue located in the methyllysine binding aromatic cage provides AGDP3 with pH-dependent H3K9me2 binding capacity.Our results uncover a molecular mechanism for the regulation of DNA demethylation by the gene silencing mark H3K9me2.
基金supported by the grant from the NIH to Z.Z.(DP5OD021355)the National Natural Science Foundation of China(91940302 and 31870741 to Y.H.)。
文摘Serving as a host factor for human immunodeficiency virus(HIV)integration,LEDGF/p75 has been under extensive study as a potential target for therapy.However,as a highly conserved protein,its physiological function remains to be thoroughly elucidated.Here,we characterize the molecular function of dP75,the Drosophila homolog of LEDGF/p75,during oogenesis.dP75 binds to transcriptionally active chromatin with its PWWP domain.The C-terminus integrase-binding domain-containing region of dP75 physically interacts with the histone kinase Jil-1 and stabilizes it in vivo.Together with Jil-1,dP75 prevents the spreading of the heterochromatin mark-H3 K9 me2-onto genes required for oogenesis and piRNA production.Without dP75,ectopical silencing of these genes disrupts oogenesis,activates transposons,and causes animal sterility.We propose that dP75,the homolog of an HIV host factor in Drosophila,partners with and stabilizes Jil-1 to ensure gene expression during oogenesis by preventing ectopic heterochromatin spreading.
基金supported by the National Key R&D Program of China(Grant No.2018YFC1003500 awarded to BW)the National Natural Science Foundation of China(Grant No.31771435 awarded to BW)
文摘In the nucleus, chromatin is folded into hierarchical architecture that is tightly linked to various nuclear functions. However, the underlying molecular mechanisms that confer these architectures remain incompletely understood. Here, we investigated the functional roles of H3 lysine 9 dimethylation(H3 K9 me2), one of the abundant histone modifications, in three-dimensional(3 D)genome organization. Unlike in mouse embryonic stem cells, inhibition of methyltransferases G9 a and GLP in differentiated cells eliminated H3 K9 me2 predominantly at A-type(active) genomic compartments, and the level of residual H3 K9 me2 modifications was strongly associated with B-type(inactive) genomic compartments. Furthermore, chemical inhibition of G9 a/GLP in mouse hepatocytes led to decreased chromatin-nuclear lamina interactions mainly at G9 a/GLP-sensitive regions, increased degree of genomic compartmentalization, and up-regulation of hundreds of genes that were associated with alterations of the 3 D chromatin. Collectively, our data demonstrated essential roles of H3 K9 me2 in 3 D genome organization.
基金supported by the National Natural Science Foundation of China (31761163001, 31701128)
文摘Cells need to appropriately balance transcriptional stability and adaptability in order to maintain their identities while responding robustly to various stimuli. Eukaryotic cells use an elegant "epigenetic" system to achieve this functionality. "Epigenetics" is referred to as heritable information beyond the DNA sequence, including histone and DNA modifications, nc RNAs and other chromatin-related components. Here, we review the mechanisms of the epigenetic inheritance of a repressive chromatin state,with an emphasis on recent progress in the field. We emphasize that(i) epigenetic information is inherited in a relatively stable but imprecise fashion;(ii) multiple cis and trans factors are involved in the maintenance of epigenetic information during mitosis; and(iii) the maintenance of a repressive epigenetic state requires both recruitment and self-reinforcement mechanisms.These mechanisms crosstalk with each other and form interconnected feedback loops to shape a stable epigenetic system while maintaining certain degrees of flexibility.
