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Antonius J M Matzke - One of the best experts on this subject based on the ideXlab platform.

  • rna directed dna methylation mediated by drd1 and pol ivb a versatile pathway for transcriptional gene silencing in plants
    Biochimica et Biophysica Acta, 2007
    Co-Authors: Bruno Huettel, Tatsuo Kanno, Lucia Daxinger, Antonius J M Matzke, Etienne Bucher, Johannes Van Der Winden, Marjori Matzke
    Abstract:

    RNA-directed DNA methylation, which is one of several RNAi-mediated pathways in the nucleus, has been highly elaborated in the plant kingdom. RNA-directed DNA methylation requires for the most part conventional DNA methyltransferases, histone modifying Enzymes and RNAi proteins; however, several novel, plant-specific proteins that are essential for this process have been identified recently. DRD1 (defective in RNA-directed DNA methylation) is a putative SWI2/SNF2-like chromatin remodelling protein; DRD2 and DRD3 (renamed NRPD2a and NRPD1b, respectively) are subunits of Pol IVb, a putative RNA polymerase found only in plants. Interestingly, DRD1 and Pol IVb appear to be required not only for RNA-directed de novo methylation, but also for full erasure of methylation when the RNA trigger is withdrawn. These proteins thus have the potential to facilitate dynamic regulation of DNA methylation. Prominent targets of RNA-directed DNA methylation in the Arabidopsis thaliana genome include retrotransposon long terminal repeats (LTRs), which have bidirectional promoter/enhancer activities, and other types of intergenic transposons and repeats. Intergenic solitary LTRs that are targeted for reversible methylation by the DRD1/Pol IVb pathway can potentially act as switches or rheostats for neighboring plant genes. The resulting alterations in gene expression patterns may promote physiological flexibility and adaptation to the environment.

  • atypical rna polymerase subunits required for rna directed dna methylation
    Nature Genetics, 2005
    Co-Authors: Tatsuo Kanno, Bruno Huettel, Florian M Mette, Werner Aufsatz, Estelle Jaligot, Lucia Daxinger, David P Kreil, Marjori Matzke, Antonius J M Matzke
    Abstract:

    RNA-directed DNA methylation, one of several RNA interference–mediated pathways in the nucleus1, has been documented in plants2,3 and in human cells4,5. Despite progress in identifying the DNA methyltransferases, Histone-Modifying Enzymes and RNA interference proteins needed for RNA-directed DNA methylation1, the mechanism remains incompletely understood. We screened for mutants defective in RNA-directed DNA methylation and silencing of a transgene promoter in Arabidopsis thaliana and identified three drd complementation groups6. DRD1 is a SNF2-like protein6 required for RNA-directed de novo methylation. We report here that DRD2 and DRD3 correspond to the second-largest subunit and largest subunit, respectively, of a fourth class of DNA-dependent RNA polymerase (polymerase IV) that is unique to plants. DRD3 is a functionally diversified homolog of NRPD1a or SDE4, identified in a separate screen for mutants defective in post-transcriptional gene silencing7,8. The identical DNA methylation patterns observed in all three drd mutants suggest that DRD proteins cooperate to create a substrate for RNA-directed de novo methylation.

  • atypical rna polymerase subunits required for rna directed dna methylation
    Nature Genetics, 2005
    Co-Authors: Tatsuo Kanno, Florian M Mette, Werner Aufsatz, David P Kreil, Marjori Matzke, Uno Huettel, Estelle Jaligo, Lucia Daxinge, Antonius J M Matzke
    Abstract:

    RNA-directed DNA methylation, one of several RNA interference–mediated pathways in the nucleus1, has been documented in plants2,3 and in human cells4,5. Despite progress in identifying the DNA methyltransferases, Histone-Modifying Enzymes and RNA interference proteins needed for RNA-directed DNA methylation1, the mechanism remains incompletely understood. We screened for mutants defective in RNA-directed DNA methylation and silencing of a transgene promoter in Arabidopsis thaliana and identified three drd complementation groups6. DRD1 is a SNF2-like protein6 required for RNA-directed de novo methylation. We report here that DRD2 and DRD3 correspond to the second-largest subunit and largest subunit, respectively, of a fourth class of DNA-dependent RNA polymerase (polymerase IV) that is unique to plants. DRD3 is a functionally diversified homolog of NRPD1a or SDE4, identified in a separate screen for mutants defective in post-transcriptional gene silencing7,8. The identical DNA methylation patterns observed in all three drd mutants suggest that DRD proteins cooperate to create a substrate for RNA-directed de novo methylation.

Marjori Matzke - One of the best experts on this subject based on the ideXlab platform.

  • rna directed dna methylation mediated by drd1 and pol ivb a versatile pathway for transcriptional gene silencing in plants
    Biochimica et Biophysica Acta, 2007
    Co-Authors: Bruno Huettel, Tatsuo Kanno, Lucia Daxinger, Antonius J M Matzke, Etienne Bucher, Johannes Van Der Winden, Marjori Matzke
    Abstract:

    RNA-directed DNA methylation, which is one of several RNAi-mediated pathways in the nucleus, has been highly elaborated in the plant kingdom. RNA-directed DNA methylation requires for the most part conventional DNA methyltransferases, histone modifying Enzymes and RNAi proteins; however, several novel, plant-specific proteins that are essential for this process have been identified recently. DRD1 (defective in RNA-directed DNA methylation) is a putative SWI2/SNF2-like chromatin remodelling protein; DRD2 and DRD3 (renamed NRPD2a and NRPD1b, respectively) are subunits of Pol IVb, a putative RNA polymerase found only in plants. Interestingly, DRD1 and Pol IVb appear to be required not only for RNA-directed de novo methylation, but also for full erasure of methylation when the RNA trigger is withdrawn. These proteins thus have the potential to facilitate dynamic regulation of DNA methylation. Prominent targets of RNA-directed DNA methylation in the Arabidopsis thaliana genome include retrotransposon long terminal repeats (LTRs), which have bidirectional promoter/enhancer activities, and other types of intergenic transposons and repeats. Intergenic solitary LTRs that are targeted for reversible methylation by the DRD1/Pol IVb pathway can potentially act as switches or rheostats for neighboring plant genes. The resulting alterations in gene expression patterns may promote physiological flexibility and adaptation to the environment.

  • atypical rna polymerase subunits required for rna directed dna methylation
    Nature Genetics, 2005
    Co-Authors: Tatsuo Kanno, Bruno Huettel, Florian M Mette, Werner Aufsatz, Estelle Jaligot, Lucia Daxinger, David P Kreil, Marjori Matzke, Antonius J M Matzke
    Abstract:

    RNA-directed DNA methylation, one of several RNA interference–mediated pathways in the nucleus1, has been documented in plants2,3 and in human cells4,5. Despite progress in identifying the DNA methyltransferases, Histone-Modifying Enzymes and RNA interference proteins needed for RNA-directed DNA methylation1, the mechanism remains incompletely understood. We screened for mutants defective in RNA-directed DNA methylation and silencing of a transgene promoter in Arabidopsis thaliana and identified three drd complementation groups6. DRD1 is a SNF2-like protein6 required for RNA-directed de novo methylation. We report here that DRD2 and DRD3 correspond to the second-largest subunit and largest subunit, respectively, of a fourth class of DNA-dependent RNA polymerase (polymerase IV) that is unique to plants. DRD3 is a functionally diversified homolog of NRPD1a or SDE4, identified in a separate screen for mutants defective in post-transcriptional gene silencing7,8. The identical DNA methylation patterns observed in all three drd mutants suggest that DRD proteins cooperate to create a substrate for RNA-directed de novo methylation.

  • atypical rna polymerase subunits required for rna directed dna methylation
    Nature Genetics, 2005
    Co-Authors: Tatsuo Kanno, Florian M Mette, Werner Aufsatz, David P Kreil, Marjori Matzke, Uno Huettel, Estelle Jaligo, Lucia Daxinge, Antonius J M Matzke
    Abstract:

    RNA-directed DNA methylation, one of several RNA interference–mediated pathways in the nucleus1, has been documented in plants2,3 and in human cells4,5. Despite progress in identifying the DNA methyltransferases, Histone-Modifying Enzymes and RNA interference proteins needed for RNA-directed DNA methylation1, the mechanism remains incompletely understood. We screened for mutants defective in RNA-directed DNA methylation and silencing of a transgene promoter in Arabidopsis thaliana and identified three drd complementation groups6. DRD1 is a SNF2-like protein6 required for RNA-directed de novo methylation. We report here that DRD2 and DRD3 correspond to the second-largest subunit and largest subunit, respectively, of a fourth class of DNA-dependent RNA polymerase (polymerase IV) that is unique to plants. DRD3 is a functionally diversified homolog of NRPD1a or SDE4, identified in a separate screen for mutants defective in post-transcriptional gene silencing7,8. The identical DNA methylation patterns observed in all three drd mutants suggest that DRD proteins cooperate to create a substrate for RNA-directed de novo methylation.

Tatsuo Kanno - One of the best experts on this subject based on the ideXlab platform.

  • rna directed dna methylation mediated by drd1 and pol ivb a versatile pathway for transcriptional gene silencing in plants
    Biochimica et Biophysica Acta, 2007
    Co-Authors: Bruno Huettel, Tatsuo Kanno, Lucia Daxinger, Antonius J M Matzke, Etienne Bucher, Johannes Van Der Winden, Marjori Matzke
    Abstract:

    RNA-directed DNA methylation, which is one of several RNAi-mediated pathways in the nucleus, has been highly elaborated in the plant kingdom. RNA-directed DNA methylation requires for the most part conventional DNA methyltransferases, histone modifying Enzymes and RNAi proteins; however, several novel, plant-specific proteins that are essential for this process have been identified recently. DRD1 (defective in RNA-directed DNA methylation) is a putative SWI2/SNF2-like chromatin remodelling protein; DRD2 and DRD3 (renamed NRPD2a and NRPD1b, respectively) are subunits of Pol IVb, a putative RNA polymerase found only in plants. Interestingly, DRD1 and Pol IVb appear to be required not only for RNA-directed de novo methylation, but also for full erasure of methylation when the RNA trigger is withdrawn. These proteins thus have the potential to facilitate dynamic regulation of DNA methylation. Prominent targets of RNA-directed DNA methylation in the Arabidopsis thaliana genome include retrotransposon long terminal repeats (LTRs), which have bidirectional promoter/enhancer activities, and other types of intergenic transposons and repeats. Intergenic solitary LTRs that are targeted for reversible methylation by the DRD1/Pol IVb pathway can potentially act as switches or rheostats for neighboring plant genes. The resulting alterations in gene expression patterns may promote physiological flexibility and adaptation to the environment.

  • atypical rna polymerase subunits required for rna directed dna methylation
    Nature Genetics, 2005
    Co-Authors: Tatsuo Kanno, Bruno Huettel, Florian M Mette, Werner Aufsatz, Estelle Jaligot, Lucia Daxinger, David P Kreil, Marjori Matzke, Antonius J M Matzke
    Abstract:

    RNA-directed DNA methylation, one of several RNA interference–mediated pathways in the nucleus1, has been documented in plants2,3 and in human cells4,5. Despite progress in identifying the DNA methyltransferases, Histone-Modifying Enzymes and RNA interference proteins needed for RNA-directed DNA methylation1, the mechanism remains incompletely understood. We screened for mutants defective in RNA-directed DNA methylation and silencing of a transgene promoter in Arabidopsis thaliana and identified three drd complementation groups6. DRD1 is a SNF2-like protein6 required for RNA-directed de novo methylation. We report here that DRD2 and DRD3 correspond to the second-largest subunit and largest subunit, respectively, of a fourth class of DNA-dependent RNA polymerase (polymerase IV) that is unique to plants. DRD3 is a functionally diversified homolog of NRPD1a or SDE4, identified in a separate screen for mutants defective in post-transcriptional gene silencing7,8. The identical DNA methylation patterns observed in all three drd mutants suggest that DRD proteins cooperate to create a substrate for RNA-directed de novo methylation.

  • atypical rna polymerase subunits required for rna directed dna methylation
    Nature Genetics, 2005
    Co-Authors: Tatsuo Kanno, Florian M Mette, Werner Aufsatz, David P Kreil, Marjori Matzke, Uno Huettel, Estelle Jaligo, Lucia Daxinge, Antonius J M Matzke
    Abstract:

    RNA-directed DNA methylation, one of several RNA interference–mediated pathways in the nucleus1, has been documented in plants2,3 and in human cells4,5. Despite progress in identifying the DNA methyltransferases, Histone-Modifying Enzymes and RNA interference proteins needed for RNA-directed DNA methylation1, the mechanism remains incompletely understood. We screened for mutants defective in RNA-directed DNA methylation and silencing of a transgene promoter in Arabidopsis thaliana and identified three drd complementation groups6. DRD1 is a SNF2-like protein6 required for RNA-directed de novo methylation. We report here that DRD2 and DRD3 correspond to the second-largest subunit and largest subunit, respectively, of a fourth class of DNA-dependent RNA polymerase (polymerase IV) that is unique to plants. DRD3 is a functionally diversified homolog of NRPD1a or SDE4, identified in a separate screen for mutants defective in post-transcriptional gene silencing7,8. The identical DNA methylation patterns observed in all three drd mutants suggest that DRD proteins cooperate to create a substrate for RNA-directed de novo methylation.

Chang Seob Kwon - One of the best experts on this subject based on the ideXlab platform.

  • human histone h3k79 methyltransferase dot1l protein binds actively transcribing rna polymerase ii to regulate gene expression
    Journal of Biological Chemistry, 2013
    Co-Authors: Inkyung Jung, Keunsoo Kang, Kwiwan Jeong, Chang Seob Kwon
    Abstract:

    Abstract Histone modifying Enzymes play a pivotal role in gene expression and repression. In human, DOT1L (Dot1-like) is the only known histone H3 lysine 79 methyltransferase. hDOT1L is associated with transcriptional activation, but the general mechanism connecting hDOT1L to active transcription remains largely unknown. Here, we report that hDOT1L interacts with the phosphorylated carboxyl-terminal domain (CTD) of actively transcribing RNA polymerase II (RNAPII) through a region conserved uniquely in multicellular DOT1 proteins. Genome-wide profiling analyses indicate that the occupancy of hDOT1L largely overlaps with that of RNAPII at actively transcribed genes, especially surrounding transcriptional start sites, in embryonic carcinoma NCCIT cells. We also find that CTD binding or H3K79 methylations by hDOT1L is important for the expression of target genes such as NANOG and OCT4 and a marker for pluripotency in NCCIT cells. Our results indicate that a functional interaction between hDOT1L and RNAPII targets hDOT1L and subsequent H3K79 methylations to actively transcribed genes.

  • human histone h3k79 methyltransferase dot1l methyltransferase binds actively transcribing rna polymerase ii to regulate gene expression
    Journal of Biological Chemistry, 2012
    Co-Authors: Inkyung Jung, Keunsoo Kang, Kwiwan Jeong, Chang Seob Kwon
    Abstract:

    Abstract Histone-Modifying Enzymes play a pivotal role in gene expression and repression. In human, DOT1L (Dot1-like) is the only known histone H3 lysine 79 methyltransferase. hDOT1L is associated with transcriptional activation, but the general mechanism connecting hDOT1L to active transcription remains largely unknown. Here, we report that hDOT1L interacts with the phosphorylated C-terminal domain of actively transcribing RNA polymerase II (RNAPII) through a region conserved uniquely in multicellular DOT1 proteins. Genome-wide profiling analyses indicate that the occupancy of hDOT1L largely overlaps with that of RNAPII at actively transcribed genes, especially surrounding transcriptional start sites, in embryonic carcinoma NCCIT cells. We also find that C-terminal domain binding or H3K79 methylations by hDOT1L is important for the expression of target genes such as NANOG and OCT4 and a marker for pluripotency in NCCIT cells. Our results indicate that a functional interaction between hDOT1L and RNAPII targets hDOT1L and subsequent H3K79 methylations to actively transcribed genes.

Jutta Kirfel - One of the best experts on this subject based on the ideXlab platform.

  • lysine specific demethylase 1 lsd1 and histone deacetylase 1 hdac1 synergistically repress proinflammatory cytokines and classical complement pathway components
    Biochemical and Biophysical Research Communications, 2012
    Co-Authors: Andreas Janzer, Reinhard Buettner, Soyoung Lim, Florian Fronhoffs, Naima Niazy, Jutta Kirfel
    Abstract:

    Histone modifying Enzymes confer epigenetic marks, directing the changes in gene expression required for diverse cellular processes. Lysine-specific demethylase 1 (LSD1) functions as a transcriptional coregulator by demethylating histone H3 on lysine 4 and lysine 9. Analyzing transcriptomes on microarrays, we identified genes which represent inflammatory-related targets of LSD1. We demonstrate a repressive role of LSD1 in proinflammatory cytokine expression such as IL1α, IL1β, IL6 and IL8 and classical complement components. Consistently, LSD1 occupies and regulates the promoter of these genes. In addition, we demonstrate that HDAC1 and LSD1 synergistically regulate these inflammatory-related genes. Our data reveal a novel role for LSD1 in suppressing immune responses.