Differential Regulation of Strand-Specific Transcripts from Arabidopsis Centromeric Satellite Repeats
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  • {"files"=>["https://ndownloader.figshare.com/files/960551"], "description"=>"<p>Total RNA was purified from plants of the indicated genotypes, and small RNAs were enriched by solubility in PEG (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010079#s4\" target=\"_blank\">Materials and Methods</a>). Mutants and WT (wt) were in the Landsberg <i>erecta</i> background (A) or the Columbia background (B). RNA was prepared from aerial tissues from 28-day-old plants.</p>", "links"=>[], "tags"=>["centromeric"], "article_id"=>630561, "categories"=>["Genetics", "Plant Biology"], "users"=>["Bruce P May", "Zachary B Lippman", "Yuda Fang", "David L Spector", "Robert A Martienssen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0010079.g005", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_siRNAs_from_Centromeric_Repeats_/630561", "title"=>"siRNAs from Centromeric Repeats", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:51:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/960648"], "description"=>"<div><p>(A) New tandemly arranged repeats are transcribed on one strand and processed by RNAi.</p><p>(B) Older repeats accumulate retrotransposon insertions that interrupt and silence the transcripts via MET1, HDA6, and DDM1.</p><p>(C) In <i>met1, hda6,</i> or <i>ddm1</i> mutants, the silencing complex is lost and promoters from retrotransposon LTRs drive transcription from both strands. cen180 repeats are blue chevrons, and retrotransposons are green boxes (not to scale).</p></div>", "links"=>[], "tags"=>["centromeric"], "article_id"=>630658, "categories"=>["Genetics", "Plant Biology"], "users"=>["Bruce P May", "Zachary B Lippman", "Yuda Fang", "David L Spector", "Robert A Martienssen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0010079.g006", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Model_for_the_Regulation_and_Evolution_of_Centromeric_Satellite_Repeat_Transcripts_/630658", "title"=>"A Model for the Regulation and Evolution of Centromeric Satellite Repeat Transcripts", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:51:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/960229"], "description"=>"<div><p>(A) cen180 repeats and oligonucleotide primers used in RT-PCR. C1, C2, and C3 are regions of conserved DNA sequence; V is a region of variable sequence. Fc and Rc primers were selected from the conserved regions.</p><p>(B) RT-PCR of cen180 and 106B repeat transcripts. RT was performed using the primers indicated, followed by PCR with the first primer and a corresponding primer on the other strand. Fc and Rc detect transcripts derived from both strands of bulk repeats, but the F primer detects strand-specific transcripts belonging to a subfamily of these repeats. Primers recognizing <i>ACTIN2</i> transcripts served as positive controls. Negative controls lacking reverse transcriptase (“no RT”) tested for DNA contamination.</p></div>", "links"=>[], "tags"=>["centromeric", "repeats", "landsberg"], "article_id"=>630237, "categories"=>["Genetics", "Plant Biology"], "users"=>["Bruce P May", "Zachary B Lippman", "Yuda Fang", "David L Spector", "Robert A Martienssen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0010079.g001", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transcripts_from_Centromeric_Repeats_in_Landsberg_erecta_/630237", "title"=>"Transcripts from Centromeric Repeats in Landsberg <i>erecta</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:48:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/472251", "https://ndownloader.figshare.com/files/472277", "https://ndownloader.figshare.com/files/472317", "https://ndownloader.figshare.com/files/472371", "https://ndownloader.figshare.com/files/472412", "https://ndownloader.figshare.com/files/472464"], "description"=>"<div><p>Centromeres interact with the spindle apparatus to enable chromosome disjunction and typically contain thousands of tandemly arranged satellite repeats interspersed with retrotransposons. While their role has been obscure, centromeric repeats are epigenetically modified and centromere specification has a strong epigenetic component. In the yeast <em>Schizosaccharomyces pombe,</em> long heterochromatic repeats are transcribed and contribute to centromere function via RNA interference (RNAi). In the higher plant <em>Arabidopsis thaliana,</em> as in mammalian cells, centromeric satellite repeats are short (180 base pairs), are found in thousands of tandem copies, and are methylated. We have found transcripts from both strands of canonical, bulk <em>Arabidopsis</em> repeats. At least one subfamily of 180–base pair repeats is transcribed from only one strand and regulated by RNAi and histone modification. A second subfamily of repeats is also silenced, but silencing is lost on both strands in mutants in the CpG DNA methyltransferase MET1, the histone deacetylase HDA6/SIL1, or the chromatin remodeling ATPase DDM1. This regulation is due to transcription from <em>Athila2</em> retrotransposons, which integrate in both orientations relative to the repeats, and differs between strains of <em>Arabidopsis.</em> Silencing lost in <em>met1</em> or <em>hda6</em> is reestablished in backcrosses to wild-type, but silencing lost in RNAi mutants and <em>ddm1</em> is not. Twenty-four–nucleotide small interfering RNAs from centromeric repeats are retained in <em>met1</em> and <em>hda6,</em> but not in <em>ddm1,</em> and may have a role in this epigenetic inheritance. Histone H3 lysine-9 dimethylation is associated with both classes of repeats. We propose roles for transcribed repeats in the epigenetic inheritance and evolution of centromeres.</p></div>", "links"=>[], "tags"=>["differential", "strand-specific", "transcripts", "centromeric", "repeats"], "article_id"=>153115, "categories"=>["Genetics", "Cell Biology"], "users"=>["Bruce P May", "Zachary B Lippman", "Yuda Fang", "David L Spector", "Robert A Martienssen"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.0010079.sg001", "https://dx.doi.org/10.1371/journal.pgen.0010079.sg002", "https://dx.doi.org/10.1371/journal.pgen.0010079.sg003", "https://dx.doi.org/10.1371/journal.pgen.0010079.sg004", "https://dx.doi.org/10.1371/journal.pgen.0010079.sg005", "https://dx.doi.org/10.1371/journal.pgen.0010079.st001"], "stats"=>{"downloads"=>15, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Differential_Regulation_of_Strand_Specific_Transcripts_from_Arabidopsis_Centromeric_Satellite_Repeats/153115", "title"=>"Differential Regulation of Strand-Specific Transcripts from <em>Arabidopsis</em> Centromeric Satellite Repeats", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-01-20 10:52:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/960400"], "description"=>"<div><p>(A) Strand-specific RT-PCR of cen180 repeats. RT was performed with forward and reverse primers indicated to the left of each panel. Mutants in DNA methylation <i>(cmt3, met1),</i> chromatin remodeling <i>(ddm1),</i> histone modification <i>(kyp, hda6),</i> and RNAi <i>(dcl1, ago1)</i> were in the Landsberg <i>erecta</i> (Ler) ecotype. <i>rdr2</i> and <i>dcl3</i> were in the Columbia background. m indicates homozygous mutants and b indicates backcrosses of mutants to WT (wt). Positive controls were primers recognizing the <i>ACTIN2</i> gene; negative controls lacked reverse transcriptase (no RT).</p><p>(B) Restriction site analysis of repeats. Repeats were amplified by cen180 F+R primers from genomic DNA (lanes 1), cDNA from <i>met1</i> mutants (lanes 2), and cDNA from <i>dcl1</i> mutants (lanes 3). Repeats in genomic DNA that have <i>TaqI</i> sites are not transcribed in either mutant, while those with Sau3AI sites are not transcribed in <i>dcl1</i>.</p><p>(C) Oligonucleotide probes specific for the subfamilies of F + R cen180 repeats expressed in <i>dcl1</i> and <i>met1</i> mutants.</p><p>(D) Strand-specific RT-PCR of cen180 repeats. RT was performed with F or R primers as in (A). Southern hybridization of these products with specific oligonucleotide probes distinguished subfamilies of repeats that were differentially regulated.</p><p>(E) Detection of read-through transcripts between cen180 and 106B repeats by strand-specific RT-PCR. 106B Fout (lane 1) and cen180 F (lane 2) primers were used to prime cDNA, followed by PCR amplification. The configuration of the transcripts is shown below each lane. Other combinations of primers did not give detectable products. RNA was prepared from aerial tissues from 28-day-old plants.</p></div>", "links"=>[], "tags"=>["centromeric"], "article_id"=>630412, "categories"=>["Genetics", "Plant Biology"], "users"=>["Bruce P May", "Zachary B Lippman", "Yuda Fang", "David L Spector", "Robert A Martienssen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0010079.g003", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Regulation_of_Centromeric_Transcripts_/630412", "title"=>"Regulation of Centromeric Transcripts", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:50:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/960487"], "description"=>"<p>Primers were designed to recognize sample cen180 cDNAs from <i>dcl1</i> and <i>met1</i> mutants of Landsberg <i>erecta</i> (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010079#pgen-0010079-g003\" target=\"_blank\">Figure 3</a>C) and <i>dcl3</i> and <i>met1</i> mutants of Columbia. PCR amplification using genomic DNA templates (DNA) tested for the presence of the particular repeats in the genome of each ecotype. RT-PCRs using RNA detected transcripts in WT (wt) and mutants of each ecotype as indicated. The cen180 Fc + Rc primers served as positive controls in the presence of reverse transcriptase and negative controls in its absence. RNA was prepared from aerial tissues from 28-day-old plants.</p>", "links"=>[], "tags"=>["cen180"], "article_id"=>630493, "categories"=>["Genetics", "Plant Biology"], "users"=>["Bruce P May", "Zachary B Lippman", "Yuda Fang", "David L Spector", "Robert A Martienssen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0010079.g004", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Polymorphic_Regulation_of_cen180_Transcripts_/630493", "title"=>"Polymorphic Regulation of cen180 Transcripts", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:50:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/960313"], "description"=>"<div><p>(A) Inflorescence meristem and developing buds probed with digoxigenin-labeled F strand of cen180 F + R PCR products and (B) probed with R strand. Mature tissue about 5 mm below the meristem (C) probed with F strand of cen180 and (D) probed with R strand. The scale bars are 50 μm.</p><p>(E) More highly magnified view of nuclei from developing buds probed with F strand (scale bar is 10 μm).</p></div>", "links"=>[], "tags"=>["situ", "hybridization", "centromeric", "probes", "longitudinal", "sections"], "article_id"=>630319, "categories"=>["Genetics", "Plant Biology"], "users"=>["Bruce P May", "Zachary B Lippman", "Yuda Fang", "David L Spector", "Robert A Martienssen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0010079.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_Situ_Hybridization_of_Centromeric_Probes_with_Longitudinal_Sections_of_Inflorescences_/630319", "title"=>"In Situ Hybridization of Centromeric Probes with Longitudinal Sections of Inflorescences", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:49:18"}

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  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"3", "full-text"=>"1", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}

Relative Metric

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