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Search Results: 1 - 10 of 176109 matches for " Steven E. Jacobsen "
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SHH1, a Homeodomain Protein Required for DNA Methylation, As Well As RDR2, RDM4, and Chromatin Remodeling Factors, Associate with RNA Polymerase IV
Julie A. Law,Ajay A. Vashisht,James A. Wohlschlegel ,Steven E. Jacobsen
PLOS Genetics , 2011, DOI: 10.1371/journal.pgen.1002195
Abstract: DNA methylation is an evolutionarily conserved epigenetic modification that is critical for gene silencing and the maintenance of genome integrity. In Arabidopsis thaliana, the de novo DNA methyltransferase, DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), is targeted to specific genomic loci by 24 nt small interfering RNAs (siRNAs) through a pathway termed RNA–directed DNA methylation (RdDM). Biogenesis of the targeting siRNAs is thought to be initiated by the activity of the plant-specific RNA polymerase IV (Pol-IV). However, the mechanism through which Pol-IV is targeted to specific genomic loci and whether factors other than the core Pol-IV machinery are required for Pol-IV activity remain unknown. Through the affinity purification of NUCLEAR RNA POLYMERASE D1 (NRPD1), the largest subunit of the Pol-IV polymerase, we found that several previously identified RdDM components co-purify with Pol-IV, namely RNA–DEPENDENT RNA POLYMERASE 2 (RDR2), CLASSY1 (CLSY1), and RNA–DIRECTED DNA METHYLATION 4 (RDM4), suggesting that the upstream siRNA generating portion of the RdDM pathway may be more physically coupled than previously envisioned. A homeodomain protein, SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1), was also found to co-purify with NRPD1; and we demonstrate that SHH1 is required for de novo and maintenance DNA methylation, as well as for the accumulation of siRNAs at specific loci, confirming it is a bonafide component of the RdDM pathway.
SRA-Domain Proteins Required for DRM2-Mediated De Novo DNA Methylation
Lianna M. Johnson,Julie A. Law,Anuj Khattar,Ian R. Henderson,Steven E. Jacobsen
PLOS Genetics , 2008, DOI: 10.1371/journal.pgen.1000280
Abstract: De novo DNA methylation and the maintenance of DNA methylation in asymmetrical sequence contexts is catalyzed by homologous proteins in plants (DRM2) and animals (DNMT3a/b). In plants, targeting of DRM2 depends on small interfering RNAs (siRNAs), although the molecular details are still unclear. Here, we show that two SRA-domain proteins (SUVH9 and SUVH2) are also essential for DRM2-mediated de novo and maintenance DNA methylation in Arabidopsis thaliana. At some loci, SUVH9 and SUVH2 act redundantly, while at other loci only SUVH2 is required, and this locus specificity correlates with the differing DNA-binding affinity of the SRA domains within SUVH9 and SUVH2. Specifically, SUVH9 preferentially binds methylated asymmetric sites, while SUVH2 preferentially binds methylated CG sites. The suvh9 and suvh2 mutations do not eliminate siRNAs, suggesting a role for SUVH9 and SUVH2 late in the RNA-directed DNA methylation pathway. With these new results, it is clear that SRA-domain proteins are involved in each of the three pathways leading to DNA methylation in Arabidopsis.
Dynamic Regulation of ARGONAUTE4 within Multiple Nuclear Bodies in Arabidopsis thaliana
Carey F Li,Ian R Henderson,Liang Song,Nina Fedoroff,Thierry Lagrange,Steven E Jacobsen
PLOS Genetics , 2008, DOI: 10.1371/journal.pgen.0040027
Abstract: DNA methylation directed by 24-nucleotide small RNAs involves the small RNA-binding protein ARGONAUTE4 (AGO4), and it was previously shown that AGO4 localizes to nucleolus-adjacent Cajal bodies, sites of snRNP complex maturation. Here we demonstrate that AGO4 also localizes to a second class of nuclear bodies, called AB-bodies, which are found immediately adjacent to condensed 45S ribosomal DNA (rDNA) sequences. AB-bodies also contain other proteins involved in RNA-directed DNA methylation including NRPD1b (a subunit of the RNA Polymerase IV complex, RNA PolIV), NRPD2 (a second subunit of this complex), and the DNA methyltransferase DRM2. These two classes of AGO4 bodies are structurally independent—disruption of one class does not affect the other—suggesting a dynamic regulation of AGO4 within two distinct nuclear compartments in Arabidopsis. Abolishing Cajal body formation in a coilin mutant reduced overall AGO4 protein levels, and coilin dicer-like3 double mutants showed a small decrease in DNA methylation beyond that seen in dicer-like3 single mutants, suggesting that Cajal bodies are required for a fully functioning DNA methylation system in Arabidopsis.
Genome-Wide Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana
Yana V. Bernatavichute, Xiaoyu Zhang, Shawn Cokus, Matteo Pellegrini, Steven E. Jacobsen
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003156
Abstract: Methylation of histone H3 lysine 9 (H3K9) is a hallmark of transcriptional silencing in many organisms. In Arabidopsis thaliana, dimethylation of H3K9 (H3K9m2) is important in the silencing of transposons and in the control of DNA methylation. We constructed a high-resolution genome-wide map of H3K9m2 methylation by using chromatin immunoprecipitation coupled with whole genome Roche Nimblegen microarrays (ChIP-chip). We observed a very high coincidence between H3K9m2 and CHG methylation (where H is either A,T or C) throughout the genome. The coding regions of genes that are associated exclusively with methylation in a CG context did not contain H3K9m2. In addition, we observed two distinct patterns of H3K9m2. Transposons and other repeat elements present in the euchromatic arms contained small islands of H3K9m2 present at relatively low levels. In contrast, pericentromeric/centromeric regions of Arabidopsis chromosomes contained long, rarely interrupted blocks of H3K9m2 present at much higher average levels than seen in the chromosome arms. These results suggest a complex interplay between H3K9m2 and different types of DNA methylation and suggest that distinct mechanisms control H3K9m2 in different compartments of the genome.
Two-Step Recruitment of RNA-Directed DNA Methylation to Tandem Repeats
Simon W.-L Chan,Xiaoyu Zhang,Yana V. Bernatavichute,Steven E. Jacobsen
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0040363
Abstract: Tandem repeat sequences are frequently associated with gene silencing phenomena. The Arabidopsis thaliana FWA gene contains two tandem repeats and is an efficient target for RNA-directed de novo DNA methylation when it is transformed into plants. We showed that the FWA tandem repeats are necessary and sufficient for de novo DNA methylation and that repeated character rather than intrinsic sequence is likely important. Endogenous FWA can adopt either of two stable epigenetic states: methylated and silenced or unmethylated and active. Surprisingly, we found small interfering RNAs (siRNAs) associated with FWA in both states. Despite this, only the methylated form of endogenous FWA could recruit further RNA-directed DNA methylation or cause efficient de novo methylation of transgenic FWA. This suggests that RNA-directed DNA methylation occurs in two steps: first, the initial recruitment of the siRNA-producing machinery, and second, siRNA-directed DNA methylation either in cis or in trans. The efficiency of this second step varies depending on the nature of the siRNA-producing locus, and at some loci, it may require pre-existing chromatin modifications such as DNA methylation itself. Enhancement of RNA-directed DNA methylation by pre-existing DNA methylation could create a self-reinforcing system to enhance the stability of silencing. Tandem repeats throughout the Arabidopsis genome produce siRNAs, suggesting that repeat acquisition may be a general mechanism for the evolution of gene silencing.
Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis
Xiaoyu Zhang,Oliver Clarenz,Shawn Cokus,Yana V. Bernatavichute,Matteo Pellegrini,Justin Goodrich,Steven E. Jacobsen
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0050129
Abstract: Trimethylation of histone H3 lysine 27 (H3K27me3) plays critical roles in regulating animal development, and in several cases, H3K27me3 is also required for the proper expression of developmentally important genes in plants. However, the extent to which H3K27me3 regulates plant genes on a genome-wide scale remains unknown. In addition, it is not clear whether the establishment and spreading of H3K27me3 occur through the same mechanisms in plants and animals. We identified regions containing H3K27me3 in the genome of the flowering plant Arabidopsis thaliana using a high-density whole-genome tiling microarray. The results suggest that H3K27me3 is a major silencing mechanism in plants that regulates an unexpectedly large number of genes in Arabidopsis (~4,400), and that the maintenance of H3K27me3 is largely independent of other epigenetic pathways, such as DNA methylation or RNA interference. Unlike in animals, where H3K27m3 occupies large genomic regions, in Arabidopsis, we found that H3K27m3 domains were largely restricted to the transcribed regions of single genes. Furthermore, unlike in animals systems, H3K27m3 domains were not preferentially associated with low–nucleosome density regions. The results suggest that different mechanisms may underlie the establishment and spreading of H3K27me3 in plants and animals.
Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana
Xiaoyu Zhang, Yana V Bernatavichute, Shawn Cokus, Matteo Pellegrini, Steven E Jacobsen
Genome Biology , 2009, DOI: 10.1186/gb-2009-10-6-r62
Abstract: We have characterized the genome-wide distribution patterns of mono-, di- and trimethylation of H3K4 (H3K4me1, H3K4me2 and H3K4me3, respectively) in Arabidopsis thaliana seedlings using chromatin immunoprecipitation and high-resolution whole-genome tiling microarrays (ChIP-chip). All three types of H3K4me are found to be almost exclusively genic, and two-thirds of Arabidopsis genes contain at least one type of H3K4me. H3K4me2 and H3K4me3 accumulate predominantly in promoters and 5' genic regions, whereas H3K4me1 is distributed within transcribed regions. In addition, H3K4me3-containing genes are highly expressed with low levels of tissue specificity, but H3K4me1 or H3K4me2 may not be directly involved in transcriptional activation. Furthermore, the preferential co-localization of H3K4me3 and H3K27me3 found in mammals does not appear to occur in plants at a genome-wide level, but H3K4me2 and H3K27me3 co-localize at a higher-than-expected frequency. Finally, we found that H3K4me2/3 and DNA methylation appear to be mutually exclusive, but surprisingly, H3K4me1 is highly correlated with CG DNA methylation in the transcribed regions of genes.H3K4me plays widespread roles in regulating gene expression in plants. Although many aspects of the mechanisms and functions of H3K4me appear to be conserved among all three kingdoms, we observed significant differences in the relationship between H3K4me and transcription or other epigenetic pathways in plants and mammals.Post-translational modifications of histones play important roles in maintaining normal transcription patterns by directly or indirectly affecting the structural properties of the chromatin. Histone modifications are highly complex due to the large number of residues that can be modified as well as the variety of modification types (for example, methylation, acetylation, phosphorylation and ubiquitination, and so on) [1]. In addition, in the case of lysine methylation, a lysine residue can be mono-, di- or trimethyl
5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells
Hume Stroud, Suhua Feng, Shannon Morey Kinney, Sriharsa Pradhan, Steven E Jacobsen
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-6-r54
Abstract: Here, we have generated a genome-wide map of 5hmC in human embryonic stem cells by hmeDIP-seq, in which hydroxymethyl-DNA immunoprecipitation is followed by massively parallel sequencing. We found that 5hmC is enriched in enhancers as well as in gene bodies, suggesting a potential role for 5hmC in gene regulation. Consistent with localization of 5hmC at enhancers, 5hmC was significantly enriched in histone modifications associated with enhancers, such as H3K4me1 and H3K27ac. 5hmC was also enriched in other protein-DNA interaction sites, such as OCT4 and NANOG binding sites. Furthermore, we found that 5hmC regions tend to have an excess of G over C on one strand of DNA.Our findings suggest that 5hmC may be targeted to certain genomic regions based both on gene expression and sequence composition.Cytosine DNA methylation (5-methylcytosine (5mC)) is an epigenetic mark that is widespread in both animals and plants, and appears to play important roles in various biological processes, such as gene silencing and imprinting. Recently, studies have shown that embryonic stem cells (ESCs) and Purkinje neurons contain high levels of 5-hydroxymethylcytosine (5hmC) [1,2]. Human TET1, a 2-oxoglutarate- and Fe(II)-dependent enzyme, has been shown to catalyze the conversion of 5mC to 5hmC both in vitro and in vivo [1]. Subsequently, all mouse Tet proteins, Tet1, Tet2 and Tet3, were shown to be able to convert 5mC to 5hmC [3]. Disruption in human TET1 and TET2 is associated with diseases such as MLL-associated leukemia [4] and myeloproliferative disorders [5]. Studies have suggested that 5hmC inhibits the methyl-CpG-binding protein MeCP2 from binding DNA [6]. In addition to the exclusion of methyl-CpG-binding proteins, 5hmC may recruit unknown 5hmC binding protein(s). Moreover, because the DNA methyltransferase DNMT1 binds poorly to 5hmC [1,7], it is possible that 5hmC plays a role in excluding DNMT1 from methylating cytosines and thus may promote DNA demethylation. Importantly, 5hmC
Two-Step Recruitment of RNA-Directed DNA Methylation to Tandem Repeats
Simon W.-L Chan,Xiaoyu Zhang,Yana V Bernatavichute,Steven E Jacobsen
PLOS Biology , 2006, DOI: 10.1371/journal.pbio.0040363
Abstract: Tandem repeat sequences are frequently associated with gene silencing phenomena. The Arabidopsis thaliana FWA gene contains two tandem repeats and is an efficient target for RNA-directed de novo DNA methylation when it is transformed into plants. We showed that the FWA tandem repeats are necessary and sufficient for de novo DNA methylation and that repeated character rather than intrinsic sequence is likely important. Endogenous FWA can adopt either of two stable epigenetic states: methylated and silenced or unmethylated and active. Surprisingly, we found small interfering RNAs (siRNAs) associated with FWA in both states. Despite this, only the methylated form of endogenous FWA could recruit further RNA-directed DNA methylation or cause efficient de novo methylation of transgenic FWA. This suggests that RNA-directed DNA methylation occurs in two steps: first, the initial recruitment of the siRNA-producing machinery, and second, siRNA-directed DNA methylation either in cis or in trans. The efficiency of this second step varies depending on the nature of the siRNA-producing locus, and at some loci, it may require pre-existing chromatin modifications such as DNA methylation itself. Enhancement of RNA-directed DNA methylation by pre-existing DNA methylation could create a self-reinforcing system to enhance the stability of silencing. Tandem repeats throughout the Arabidopsis genome produce siRNAs, suggesting that repeat acquisition may be a general mechanism for the evolution of gene silencing.
DNA Methyltransferases Are Required to Induce Heterochromatic Re-Replication in Arabidopsis
Hume Stroud,Christopher J. Hale,Suhua Feng,Elena Caro,Yannick Jacob,Scott D. Michaels,Steven E. Jacobsen
PLOS Genetics , 2012, DOI: 10.1371/journal.pgen.1002808
Abstract: The relationship between epigenetic marks on chromatin and the regulation of DNA replication is poorly understood. Mutations of the H3K27 methyltransferase genes, ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 (ATXR5) and ATXR6, result in re-replication (repeated origin firing within the same cell cycle). Here we show that mutations that reduce DNA methylation act to suppress the re-replication phenotype of atxr5 atxr6 mutants. This suggests that DNA methylation, a mark enriched at the same heterochromatic regions that re-replicate in atxr5/6 mutants, is required for aberrant re-replication. In contrast, RNA sequencing analyses suggest that ATXR5/6 and DNA methylation cooperatively transcriptionally silence transposable elements (TEs). Hence our results suggest a complex relationship between ATXR5/6 and DNA methylation in the regulation of DNA replication and transcription of TEs.
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