Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis
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{"title"=>"Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis", "type"=>"journal", "authors"=>[{"first_name"=>"Xiaoyu", "last_name"=>"Zhang", "scopus_author_id"=>"55970198100"}, {"first_name"=>"Oliver", "last_name"=>"Clarenz", "scopus_author_id"=>"8661475800"}, {"first_name"=>"Shawn", "last_name"=>"Cokus", "scopus_author_id"=>"6507385391"}, {"first_name"=>"Yana V.", "last_name"=>"Bernatavichute", "scopus_author_id"=>"12800295500"}, {"first_name"=>"Matteo", "last_name"=>"Pellegrini", "scopus_author_id"=>"7103161935"}, {"first_name"=>"Justin", "last_name"=>"Goodrich", "scopus_author_id"=>"7102131372"}, {"first_name"=>"Steven E.", "last_name"=>"Jacobsen", "scopus_author_id"=>"12799754300"}], "year"=>2007, "source"=>"PLoS Biology", "identifiers"=>{"scopus"=>"2-s2.0-34249068213", "sgr"=>"34249068213", "issn"=>"15449173", "doi"=>"10.1371/journal.pbio.0050129", "pmid"=>"17439305", "isbn"=>"1545-7885 (Electronic)\\r1544-9173 (Linking)", "pui"=>"46790393"}, "id"=>"90515c49-afff-3965-b537-4c23d71cbbde", "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.", "link"=>"http://www.mendeley.com/research/wholegenome-analysis-histone-h3-lysine-27-trimethylation-arabidopsis-2", "reader_count"=>296, "reader_count_by_academic_status"=>{"Unspecified"=>8, "Professor > Associate Professor"=>9, "Librarian"=>1, "Researcher"=>69, "Student > Doctoral Student"=>19, "Student > Ph. D. Student"=>92, "Student > Postgraduate"=>17, "Student > Master"=>36, "Other"=>3, "Student > Bachelor"=>20, "Lecturer"=>4, "Professor"=>18}, "reader_count_by_user_role"=>{"Unspecified"=>8, "Professor > Associate Professor"=>9, "Librarian"=>1, "Researcher"=>69, "Student > Doctoral Student"=>19, "Student > Ph. D. Student"=>92, "Student > Postgraduate"=>17, "Student > Master"=>36, "Other"=>3, "Student > Bachelor"=>20, "Lecturer"=>4, "Professor"=>18}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>13, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>26, "Mathematics"=>1, "Agricultural and Biological Sciences"=>249, "Medicine and Dentistry"=>1, "Neuroscience"=>1, "Social Sciences"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>249}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>26}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>13}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Republic of Singapore"=>1, "United States"=>7, "Japan"=>2, "United Kingdom"=>4, "Switzerland"=>1, "Portugal"=>1, "Canada"=>1, "Netherlands"=>3, "Czech Republic"=>2, "China"=>2, "Brazil"=>1, "Poland"=>1, "Denmark"=>1, "Australia"=>1, "Germany"=>2}, "group_count"=>7}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/467506", "https://ndownloader.figshare.com/files/467514", "https://ndownloader.figshare.com/files/467523", "https://ndownloader.figshare.com/files/467544", "https://ndownloader.figshare.com/files/467560", "https://ndownloader.figshare.com/files/467595", "https://ndownloader.figshare.com/files/467602", "https://ndownloader.figshare.com/files/467617", "https://ndownloader.figshare.com/files/467631", "https://ndownloader.figshare.com/files/467653", "https://ndownloader.figshare.com/files/467664", "https://ndownloader.figshare.com/files/467670", "https://ndownloader.figshare.com/files/467690", "https://ndownloader.figshare.com/files/467698"], "description"=>"<div><p>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 <em>Arabidopsis thaliana</em> 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 <em>Arabidopsis</em> (~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 <em>Arabidopsis,</em> 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.</p> </div>", "links"=>[], "tags"=>["whole-genome", "histone", "h3", "lysine", "27", "trimethylation"], "article_id"=>152170, "categories"=>["Genetics"], "users"=>["Xiaoyu Zhang", "Oliver Clarenz", "Shawn Cokus", "Yana V Bernatavichute", "Matteo Pellegrini", "Justin Goodrich", "Steven E Jacobsen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.0050129.sd001", "https://dx.doi.org/10.1371/journal.pbio.0050129.sd002", "https://dx.doi.org/10.1371/journal.pbio.0050129.sg001", "https://dx.doi.org/10.1371/journal.pbio.0050129.sg002", "https://dx.doi.org/10.1371/journal.pbio.0050129.sg003", "https://dx.doi.org/10.1371/journal.pbio.0050129.sg004", "https://dx.doi.org/10.1371/journal.pbio.0050129.sg005", "https://dx.doi.org/10.1371/journal.pbio.0050129.sg006", "https://dx.doi.org/10.1371/journal.pbio.0050129.sg007", "https://dx.doi.org/10.1371/journal.pbio.0050129.sg008", "https://dx.doi.org/10.1371/journal.pbio.0050129.sg009", "https://dx.doi.org/10.1371/journal.pbio.0050129.sg010", "https://dx.doi.org/10.1371/journal.pbio.0050129.st001", "https://dx.doi.org/10.1371/journal.pbio.0050129.st002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Whole_Genome_Analysis_of_Histone_H3_Lysine_27_Trimethylation_in_Arabidopsis_/152170", "title"=>"Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in <em>Arabidopsis</em>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-04-17 00:36:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/950483"], "description"=>"<div><p>(A) Comparison of ChIP-chip results with <i>Arabidopsis</i> genes (red boxes, where arrows indicate direction of transcription) that were previously shown to be H3K27me3 targets [<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050129#pbio-0050129-b021\" target=\"_blank\">21</a>–<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050129#pbio-0050129-b027\" target=\"_blank\">27</a>]. Genes are shown as green boxes (exons) and lines (introns), and H3K27me3 is shown as vertical light blue bars [posterior probability ranging from 0 (bottom) to 1 (top)]. Orange scale bars represent 1 kb.</p>\n <p>(B) Euchromatic chromosomal distribution of H3K27me3 regions. Top panels: the total length of repetitive sequences (<i>y-</i>axis, left-side scale) and number of genes per 100 kb (<i>y-</i>axis, right-side scale). Bottom panels: the total length of methylated DNA (<i>y-</i>axis, left-side scale) and H3K27me3 regions per 100 kb (<i>y-</i>axis, right-side scale). Arrows indicate the heterochromatic knob on chromosome 4.</p></div>", "links"=>[], "tags"=>["h3k27me3"], "article_id"=>620802, "categories"=>["Genetics"], "users"=>["Xiaoyu Zhang", "Oliver Clarenz", "Shawn Cokus", "Yana V Bernatavichute", "Matteo Pellegrini", "Justin Goodrich", "Steven E Jacobsen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.0050129.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_Wide_Identification_of_H3K27me3_Regions_/620802", "title"=>"Genome-Wide Identification of H3K27me3 Regions", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-17 00:13:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/950604"], "description"=>"<div><p>(A) Expression level of H3K27me3 target genes (red) compared to all genes (green) or genes that are not targeted by H3K27me3 (blue). Expression levels were obtained by averaging appropriate developmental stages from a recently published dataset [<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050129#pbio-0050129-b035\" target=\"_blank\">35</a>] (see <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050129#s3\" target=\"_blank\">Materials and Methods</a>). <i>x-</i>axis: expression level (log<sub>2</sub> scale, vertical bars indicate the bins used.); <i>y-</i>axis: percentage of genes with given expression level.</p>\n <p>(B) Tissue specificity of H3K27me3 target genes (red), non-H3K27me3 target genes (blue), and all genes (green), measured by entropy values (low entropy values = high tissue specificity). <i>x-</i>axis: entropy values (vertical bars indicate the bins used); <i>y</i> axis: fraction of genes with the given entropy value.</p>\n <p>(C) Cluster analysis of H3K27me3 target genes. H3K27me3 target genes are grouped into eight mutually exclusive clusters based on their expression patterns. Three clusters that are specifically expressed in roots (left), seeds/siliques (middle), and floral organs (right) are shown as here as examples. Other clusters are shown in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050129#pbio-0050129-sg003\" target=\"_blank\">Figure S3</a>. Each row represents a gene, and each column represents a tissue type. Red or green indicate tissues in which a particular gene is highly expressed or repressed, respectively. Results of GO analyses for each cluster are shown below. The “% in genome” and “% in cluster” columns indicate the percentages of genes in the genome or in the clusters with corresponding GO terms.</p></div>", "links"=>[], "tags"=>["h3k27me3"], "article_id"=>620929, "categories"=>["Genetics"], "users"=>["Xiaoyu Zhang", "Oliver Clarenz", "Shawn Cokus", "Yana V Bernatavichute", "Matteo Pellegrini", "Justin Goodrich", "Steven E Jacobsen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.0050129.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_H3K27me3_Target_Genes_/620929", "title"=>"Characteristics of H3K27me3 Target Genes", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-17 00:15:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/950725"], "description"=>"<div><p>(A) Length distribution of H3K27me3 regions [yellow: maximal gap = 200 bp (MG200); brown: maximal gap = 1,000 bp (MG1000); see <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050129#s3\" target=\"_blank\">Materials and Methods</a> for details]. <i>x-</i>axis: length of H3K27me3 regions (log<sub>10</sub> scale); <i>y-</i>axis: percentage of H3K27me3 regions with corresponding length.</p>\n <p>(B) Gene-level distribution of H3K27me3. Each gene (thick horizontal bar, shown as 2.5 kb, which is the average length of <i>Arabidopsis</i> genes) was divided into 20 intervals (5% each interval), and the 1-kb regions upstream and downstream of each gene (thin horizontal bars) were divided into 50-bp intervals. The percentage of genes with H3K27me3 in each interval was graphed (<i>y-</i>axis). Dotted line indicates the percentage of the <i>Arabidopsis</i> genome that is associated with H3K27me3 (~5.7%).</p>\n <p>(C) The number of genes covered by each H3K27me3 region (yellow: maximal gap = 200 bp; brown: maximal gap = 1,000 bp). <i>x-</i>axis: number of genes covered by a H3K27me3 region; <i>y-</i>axis: percentage of H3K27me3 regions covering a given number of genes.</p>\n <p>(D) Correlation of the expression patterns of neighboring H3K27me3 target genes (maximal gap = 1,000 bp) covered by the same H3K27me3 region (brown). All possible pair-wise correlations between H3K27me3 target genes were used as a control (gray). <i>x-</i>axis: correlation of expression patterns (1 = perfect positive correlation; −1 = perfect negative correlation; 0 = not correlated). <i>y-</i>axis: percentage of gene pairs with corresponding correlation.</p></div>", "links"=>[], "tags"=>["h3k27me3", "regions"], "article_id"=>621046, "categories"=>["Genetics"], "users"=>["Xiaoyu Zhang", "Oliver Clarenz", "Shawn Cokus", "Yana V Bernatavichute", "Matteo Pellegrini", "Justin Goodrich", "Steven E Jacobsen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.0050129.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_H3K27me3_Regions_in_Arabidopsis_/621046", "title"=>"Characteristics of H3K27me3 Regions in <i>Arabidopsis</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-17 00:17:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/950808"], "description"=>"<div><p>(A) A region of chromosome 1, showing the presence of LND regions (yellow vertical line) in promoters. Genes are shown as in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050129#pbio-0050129-g001\" target=\"_blank\">Figure 1</a>A. Red boxes indicate individual genes. Red arrows indicate the direction of transcription.</p>\n <p>(B) Euchromatic chromosomal distribution of LND regions shown as the total length of LND regions per 100 kb (left <i>y-</i>axis). Arrow indicates the heterochromatic knob on chromosome 4. Distribution of DNA methylation is shown for comparison (right <i>y-</i>axis).</p>\n <p>(C) Gene-level distribution of LND regions (solid lines, left <i>y-</i>axis) and <i>Arabidopsis</i> Gene Regulatory Information Server (AGRIS) transcription factor binding sites (dotted lines, right <i>y-</i>axis). <i>x-</i>axis is described as in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050129#pbio-0050129-g003\" target=\"_blank\">Figure 3</a>B.</p>\n <p>(D) Expression levels of genes with LND regions in their promoters (LND promoter genes, yellow) compared to non-LND genes (blue), or all genes (green).</p>\n <p>(E) Tissue specificity (shown as entropy) of LND promoter genes (yellow) compared to non-LND promoter genes (blue), or all genes (green).</p></div>", "links"=>[], "tags"=>["regions"], "article_id"=>621128, "categories"=>["Genetics"], "users"=>["Xiaoyu Zhang", "Oliver Clarenz", "Shawn Cokus", "Yana V Bernatavichute", "Matteo Pellegrini", "Justin Goodrich", "Steven E Jacobsen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.0050129.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LND_Regions_in_Arabidopsis_/621128", "title"=>"LND Regions in <i>Arabidopsis</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-17 00:18:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/950922"], "description"=>"<div><p>(A) The fraction of H3K27me3 regions and random control regions overlapping with siRNA clusters (blue).</p>\n <p>(B) The fraction of H3K27me3 regions and random control regions overlapping with DNA-methylated regions (blue).</p>\n <p>(C) The fractions of genes containing body DNA methylation (orange), promoter DNA methylation (red), and no DNA methylation (green) that are H3K27me3 targets. The genome averages of expressed genes are shown for comparison.</p></div>", "links"=>[], "tags"=>["dna"], "article_id"=>621245, "categories"=>["Genetics"], "users"=>["Xiaoyu Zhang", "Oliver Clarenz", "Shawn Cokus", "Yana V Bernatavichute", "Matteo Pellegrini", "Justin Goodrich", "Steven E Jacobsen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.0050129.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_H3K27me3_siRNAs_and_DNA_Methylation_/621245", "title"=>"Relationship between H3K27me3, siRNAs, and DNA Methylation", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-17 00:20:45"}

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Relative Metric

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