Maize Unstable factor for orange1 Is Required for Maintaining Silencing Associated with Paramutation at the pericarp color1 and booster1 Loci
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{"title"=>"Maize Unstable factor for orange1 Is Required for Maintaining Silencing Associated with Paramutation at the pericarp color1 and booster1 Loci", "type"=>"journal", "authors"=>[{"first_name"=>"Rajandeep S.", "last_name"=>"Sekhon", "scopus_author_id"=>"8324368300"}, {"first_name"=>"Po Hao", "last_name"=>"Wang", "scopus_author_id"=>"35749286400"}, {"first_name"=>"Lyudmila", "last_name"=>"Sidorenko", "scopus_author_id"=>"35520453000"}, {"first_name"=>"Vicki L.", "last_name"=>"Chandler", "scopus_author_id"=>"7005247017"}, {"first_name"=>"Surinder", "last_name"=>"Chopra", "scopus_author_id"=>"7202868763"}], "year"=>2012, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-84868136460", "pmid"=>"23055943", "sgr"=>"84868136460", "doi"=>"10.1371/journal.pgen.1002980", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "issn"=>"15537390", "pui"=>"365953657"}, "id"=>"d5cd7092-a524-33f9-961c-39cf61442ca4", "abstract"=>"To understand the molecular mechanisms underlying paramutation, we examined the role of Unstable factor for orange1 (Ufo1) in maintaining paramutation at the maize pericarp color1 (p1) and booster1 (b1) loci. Genetic tests revealed that the Ufo1-1 mutation disrupted silencing associated with paramutation at both p1 and b1. The level of up regulation achieved at b1 was lower than that at p1, suggesting differences in the role Ufo1-1 plays at these loci. We characterized the interaction of Ufo1-1 with two silenced p1 epialleles, P1-rr' and P1-pr(TP), that were derived from a common P1-rr ancestor. Both alleles are phenotypically indistinguishable, but differ in their paramutagenic activity; P1-rr' is paramutagenic to P1-rr, while P1-pr(TP) is non-paramutagenic. Analysis of cytosine methylation revealed striking differences within an enhancer fragment that is required for paramutation; P1-rr' exhibited increased methylation at symmetric (CG and CHG) and asymmetric (CHH) sites, while P1-pr(TP) was methylated only at symmetric sites. Both silenced alleles had higher levels of dimethylation of lysine 9 on histone 3 (H3K9me2), an epigenetic mark of silent chromatin, in the enhancer region. Both epialleles were reactivated in the Ufo1-1 background; however, reactivation of P1-rr' was associated with dramatic loss of symmetric and asymmetric cytosine methylation in the enhancer, while methylation of up-regulated P1-pr(TP) was not affected. Interestingly, Ufo1-1-mediated reactivation of both alleles was accompanied with loss of H3K9me2 mark from the enhancer region. Therefore, while earlier studies have shown correlation between H3K9me2 and DNA methylation, our study shows that these two epigenetic marks are uncoupled in the Ufo1-1-reactivated p1 alleles. Furthermore, while CHH methylation at the enhancer region appears to be the major distinguishing mark between paramutagenic and non-paramutagenic p1 alleles, H3K9me2 mark appears to be important for maintaining epigenetic silencing.", "link"=>"http://www.mendeley.com/research/maize-unstable-factor-orange1-required-maintaining-silencing-associated-paramutation-pericarp-color1", "reader_count"=>27, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>14, "Student > Master"=>3, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>14, "Student > Master"=>3, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>25}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>25}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}}, "reader_count_by_country"=>{"Canada"=>2, "Netherlands"=>1, "United States"=>1, "United Kingdom"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/563936"], "description"=>"<p>A. Loss of pericarp and cob glume pigmentation phenotype of <i>P1-pr<sup>TP</sup></i>. The pericarp pigmentation is present only at the silk attachment point while the cob glumes are pink. B. <i>P1-pr<sup>TP</sup></i> is highly methylated as compared to <i>P1-rr</i>. Leaf genomic DNA of <i>P1-rr</i> and <i>P1-pr<sup>TP</sup></i> was digested with <i>Hpa</i>II and sequentially hybridized with <i>p1</i> probe fragments 15 and 6 (See <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002980#pgen-1002980-g005\" target=\"_blank\">Figure 5C</a> for location of probes). Size and location of hybridizing bands in kilobase pair is indicated by arrows on the left for probe 15 and on the right for probe 6. C. Methylation map of <i>P1-rr ufo1</i> and <i>P1-pr<sup>TP</sup> ufo1</i>. Gene structure is shown at the top and the rest of the figure description is same as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002980#pgen-1002980-g003\" target=\"_blank\">Figure 3B</a>.</p>", "links"=>[], "tags"=>["epiallele", "correlated", "dna"], "article_id"=>234433, "categories"=>["Genetics", "Plant Biology"], "users"=>["Rajandeep S. Sekhon", "Po-Hao Wang", "Lyudmila Sidorenko", "Vicki L. Chandler", "Surinder Chopra"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002980.g005", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Silencing_of_P1_pr_TP_an_epiallele_of_P1_rr_is_correlated_with_DNA_methylation_/234433", "title"=>"Silencing of <i>P1-pr<sup>TP</sup></i>, an epiallele of <i>P1-rr</i>, is correlated with DNA methylation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-04 01:13:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/564134"], "description"=>"<p>ChIP assay was performed using pericarp tissues. Chromatin complex was immunoprecipitated with antibodies against H3K9me2. Mouse IgG was used as a negative control (NoAb). Quantitative PCR was performed to quantify the DNA enrichments at the P1.2 kb distal enhancer. The data presented here is the mean ± SE from three biological replicates of three independent ChIP experiments.</p>", "links"=>[], "tags"=>["h3k9-dimethylation", "levels"], "article_id"=>234631, "categories"=>["Genetics", "Plant Biology"], "users"=>["Rajandeep S. Sekhon", "Po-Hao Wang", "Lyudmila Sidorenko", "Vicki L. Chandler", "Surinder Chopra"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002980.g007", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_H3K9_dimethylation_H3K9me2_levels_in_P1_rr_8242_and_P1_pr_TP_in_the_absence_and_presence_of_Ufo1_1_/234631", "title"=>"Comparison of H3K9-dimethylation (H3K9me2) levels in <i>P1-rr′</i> and <i>P1-pr<sup>TP</sup></i> in the absence and presence of <i>Ufo1-1</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-04 01:17:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/563790"], "description"=>"<p><i>P1-rr′/p1-ww; Ufo1-1/ufo1</i> and <i>P1-pr<sup>TP</sup>/p1-ww; Ufo1-1/ufo1</i> refer to plants that showed gain of pigmentation. Bisulfite sequencing was performed on genomic DNA extracted from pericarp tissue. Genomic DNA from two independent plants per genotype was used for bisulfite sequencing. For each genotype, the percent methylation is shown on the <i>y</i>-axis while the position of cytosine residues in CG, CHG, and CHH context is shown at the <i>x</i>-axis of the bottom graph.</p>", "links"=>[], "tags"=>["methylation", "modifications", "cytosine", "residues", "443-bp", "enhancer"], "article_id"=>234280, "categories"=>["Genetics", "Plant Biology"], "users"=>["Rajandeep S. Sekhon", "Po-Hao Wang", "Lyudmila Sidorenko", "Vicki L. Chandler", "Surinder Chopra"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002980.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ufo1_1_induced_methylation_modifications_of_individual_cytosine_residues_in_the_443_bp_fragment_of_the_P1_2_enhancer_of_P1_rr_8242_and_P1_pr_TP_/234280", "title"=>"<i>Ufo1-1</i>-induced methylation modifications of individual cytosine residues in the 443-bp fragment of the P1.2 enhancer of <i>P1-rr′</i> and <i>P1-pr<sup>TP</sup></i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-04 01:11:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/563536"], "description"=>"<p>Crossing scheme is shown at the top. Tables show results of tests for <i>P1-rr′</i> paramutagenicity (on the right) and <i>Ufo1-1</i> mediated <i>P1-rr′</i> reactivation (on the left) for the same <i>P1-rr′</i> plants.</p>", "links"=>[], "tags"=>["inversely", "correlates", "reactivation"], "article_id"=>234028, "categories"=>["Genetics", "Plant Biology"], "users"=>["Rajandeep S. Sekhon", "Po-Hao Wang", "Lyudmila Sidorenko", "Vicki L. Chandler", "Surinder Chopra"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002980.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Paramutagenicity_of_P1_rr_8242_inversely_correlates_with_frequency_of_reactivation_by_Ufo1_1_/234028", "title"=>"Paramutagenicity of <i>P1-rr′</i> inversely correlates with frequency of reactivation by <i>Ufo1-1</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-04 01:07:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/563437"], "description"=>"<p>A. Pericarp and cob glume phenotypes of F<sub>1</sub> progeny plants obtained from a cross between highly suppressed <i>P1-rr′ ufo1</i> and <i>p1-ww Ufo1-1</i>. B. Heritability of <i>Ufo1-1</i>-induced reactivation of <i>P1-rr′</i>. F<sub>1</sub> plants were crossed with <i>p1-ww</i>[<i>4Co63</i>] and progeny was scored for pericarp pigmentation. Expected segregation frequencies are based on the assumption that <i>P1-rr′</i> reverts back to silenced state after segregation of <i>Ufo1-1</i>.</p>", "links"=>[], "tags"=>["mediates", "reactivation"], "article_id"=>233934, "categories"=>["Genetics", "Plant Biology"], "users"=>["Rajandeep S. Sekhon", "Po-Hao Wang", "Lyudmila Sidorenko", "Vicki L. Chandler", "Surinder Chopra"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002980.g001", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ufo1_1_mediates_reactivation_of_P1_rr_8242_/233934", "title"=>"<i>Ufo1-1</i> mediates reactivation of <i>P1-rr′</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-04 01:05:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/564050"], "description"=>"<p>A. Pericarp and cob glume pigmentation phenotypes of F<sub>1</sub> progeny obtained from a cross between <i>P1-pr<sup>TP</sup></i> and <i>p1-ww Ufo1-1</i> plants. B. Heritability of <i>Ufo1-1</i>-induced reactivation of <i>P1-pr<sup>TP</sup></i>. F<sub>1</sub> plants showing gain of pericarp pigmentation (red/variegated pericarps) were crossed with <i>p1-ww</i>[<i>4Co63</i>] and test-cross progenies were examined for pericarp and cob glume pigmentation. Expected segregation frequencies are based on assumption that increased pigmentation of <i>P1-pr<sup>TP</sup></i> allele is not heritable in the absence <i>Ufo1-1</i>.</p>", "links"=>[], "tags"=>["reactivation"], "article_id"=>234544, "categories"=>["Genetics", "Plant Biology"], "users"=>["Rajandeep S. Sekhon", "Po-Hao Wang", "Lyudmila Sidorenko", "Vicki L. Chandler", "Surinder Chopra"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002980.g006", "stats"=>{"downloads"=>2, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representative_data_showing_Ufo1_1_induced_reactivation_of_P1_pr_TP_/234544", "title"=>"Representative data showing <i>Ufo1-1</i>–induced reactivation of <i>P1-pr<sup>TP</sup></i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-04 01:15:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/563603"], "description"=>"<p>A. DNA gel blot showing methylation differences among <i>P1-rr ufo1</i>, <i>P1-rr</i>′<i>ufo1</i>, two F<sub>1</sub> sibling plants not reactivated by <i>Ufo1-1</i> (marked as N), and two F<sub>1</sub> sibling plants reactivated by <i>Ufo1-1</i> (marked as R). Leaf genomic DNA was digested with <i>Hpa</i>II endonuclease and hybridized with probe fragment 15. Molecular weight marker in kilobase pair is shown on the left, and arrows on the right show positions and sizes of the hybridizing bands. B. Methylation map of <i>P1-rr ufo1</i>, <i>P1-rr′ ufo1</i> and <i>P1-rr′ Ufo1-1</i>. Gene structure is shown at the top. A solid black line represents <i>P1-rr</i> sequence with black boxes denoting exons and open boxes indicating UTR's. Transcription start site is indicated as a bent arrow. Positions and relative sizes of the probe 15 fragments are shown as open boxes above the gene map; three relatively smaller boxes labeled as 15 are the truncated copies of probe 15. Striped box to the left of transcription start site represents the P1.2 enhancer fragment. Solid double-headed arrows below the gene map indicate the region examined by genomic bisulfite sequencing while hollow double-headed arrows represent the region analyzed by ChIP assay. Methylation map of <i>Hpa</i>II sites is shown below the gene structure. Solid line represents the <i>P1-rr</i> sequence while the short vertical lines represent <i>Hpa</i>II sites. Ovals above the <i>Hpa</i>II sites represent methylation status of individual sites; open, grey and black ovals represent non-methylated, partially methylated, and completely methylated <i>Hpa</i>II sites, respectively. Lines with double arrowheads above the methylation map represent the <i>Hpa</i>II fragments observed on the DNA gel blot; only fragments and <i>Hpa</i>II sites resolved by the restriction analysis are shown.</p>", "links"=>[], "tags"=>["cytosine", "methylation"], "article_id"=>234101, "categories"=>["Genetics", "Plant Biology"], "users"=>["Rajandeep S. Sekhon", "Po-Hao Wang", "Lyudmila Sidorenko", "Vicki L. Chandler", "Surinder Chopra"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002980.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ufo1_1_mediated_loss_of_cytosine_methylation_in_P1_rr_/234101", "title"=>"<i>Ufo1-1</i>-mediated loss of cytosine methylation in <i>P1-rr</i>′.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-04 01:08:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/564217"], "description"=>"<p>Effect of <i>Ufo1-1</i> was assayed in four consecutive backcrosses as shown in the crossing scheme in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002980#pgen.1002980.s003\" target=\"_blank\">Figure S3</a>. A. Photo panels from BC<sub>2</sub> generation showing <i>B′</i> plant pigmentation and corresponding <i>P1-wr</i> pericarp and cob glume phenotypes, which were used as phenotypic indicators of <i>Ufo1-1</i> presence. The <i>P1-wr</i> has colorless pericarp and red cob and <i>P1-pr<sup>TP</sup></i> has silk-scarred pericarp and pink cob glume in the <i>ufo1</i> genetic background. In the mutant <i>Ufo1-1/ufo1</i> background <i>P1-wr</i> and <i>P1-pr<sup>TP</sup></i> exhibit dramatic increase in pigmentation and have very dark red pericarp and cob glume. In the wild type <i>ufo1</i> background, the <i>B′</i> allele has light streaky plant pigmentation while in the <i>Ufo1-1/ufo1</i> background <i>B′</i> plants have increased pigmentation as evidenced by the presence of broad darkly pigmented sectors. This increase of <i>B′</i> pigmentation is significant because <i>B′</i> never displays any increase in pigmentation in wild type genetic backgrounds. B. Summary of the results from F<sub>1</sub> and three generations of introgression in the mutant <i>Ufo1-1/ufo1</i> background are shown.</p>", "links"=>[], "tags"=>["increases"], "article_id"=>234712, "categories"=>["Genetics", "Plant Biology"], "users"=>["Rajandeep S. Sekhon", "Po-Hao Wang", "Lyudmila Sidorenko", "Vicki L. Chandler", "Surinder Chopra"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002980.g008", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ufo1_1_increases_B_8242_pigmentation_/234712", "title"=>"<i>Ufo1-1</i> increases <i>B′</i> pigmentation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-04 01:18:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/299873", "https://ndownloader.figshare.com/files/299896", "https://ndownloader.figshare.com/files/299933"], "description"=>"<div><p>To understand the molecular mechanisms underlying paramutation, we examined the role of <em>Unstable factor for orange1</em> (<em>Ufo1</em>) in maintaining paramutation at the maize <em>pericarp color1</em> (<em>p1</em>) and <em>booster1</em> (<em>b1</em>) loci. Genetic tests revealed that the <em>Ufo1-1</em> mutation disrupted silencing associated with paramutation at both <em>p1</em> and <em>b1</em>. The level of up regulation achieved at <em>b1</em> was lower than that at <em>p1</em>, suggesting differences in the role <em>Ufo1-1</em> plays at these loci. We characterized the interaction of <em>Ufo1-1</em> with two silenced <em>p1</em> epialleles, <em>P1-rr</em>′ and <em>P1-pr<sup>TP</sup></em>, that were derived from a common <em>P1-rr</em> ancestor. Both alleles are phenotypically indistinguishable, but differ in their paramutagenic activity; <em>P1-rr′</em> is paramutagenic to <em>P1-rr</em>, while <em>P1-pr<sup>TP</sup></em> is non-paramutagenic. Analysis of cytosine methylation revealed striking differences within an enhancer fragment that is required for paramutation; <em>P1-rr</em>′ exhibited increased methylation at symmetric (CG and CHG) and asymmetric (CHH) sites, while <em>P1-pr<sup>TP</sup></em> was methylated only at symmetric sites. Both silenced alleles had higher levels of dimethylation of lysine 9 on histone 3 (H3K9me2), an epigenetic mark of silent chromatin, in the enhancer region. Both epialleles were reactivated in the <em>Ufo1-1</em> background; however, reactivation of <em>P1-rr′</em> was associated with dramatic loss of symmetric and asymmetric cytosine methylation in the enhancer, while methylation of up-regulated <em>P1-pr<sup>TP</sup></em> was not affected. Interestingly, <em>Ufo1-1</em>–mediated reactivation of both alleles was accompanied with loss of H3K9me2 mark from the enhancer region. Therefore, while earlier studies have shown correlation between H3K9me2 and DNA methylation, our study shows that these two epigenetic marks are uncoupled in the <em>Ufo1-1</em>–reactivated <em>p1</em> alleles. Furthermore, while CHH methylation at the enhancer region appears to be the major distinguishing mark between paramutagenic and non-paramutagenic <em>p1</em> alleles, H3K9me2 mark appears to be important for maintaining epigenetic silencing.</p> </div>", "links"=>[], "tags"=>["maize", "maintaining", "paramutation", "loci"], "article_id"=>119129, "categories"=>["Genetics", "Cell Biology"], "users"=>["Rajandeep S. Sekhon", "Po-Hao Wang", "Lyudmila Sidorenko", "Vicki L. Chandler", "Surinder Chopra"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002980.s001", "https://dx.doi.org/10.1371/journal.pgen.1002980.s002", "https://dx.doi.org/10.1371/journal.pgen.1002980.s003"], "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Maize_Unstable_factor_for_orange1_Is_Required_for_Maintaining_Silencing_Associated_with_Paramutation_at_the_pericarp_color1_and_booster1_Loci/119129", "title"=>"Maize <em>Unstable factor for orange1</em> Is Required for Maintaining Silencing Associated with Paramutation at the <em>pericarp color1</em> and <em>booster1</em> Loci", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-10-04 02:32:09"}

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Relative Metric

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