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{"title"=>"ATX1-Generated H3K4me3 Is Required for Efficient Elongation of Transcription, Not Initiation, at ATX1-Regulated Genes", "type"=>"journal", "authors"=>[{"first_name"=>"Yong", "last_name"=>"Ding", "scopus_author_id"=>"36143867800"}, {"first_name"=>"Ivan", "last_name"=>"Ndamukong", "scopus_author_id"=>"16069218900"}, {"first_name"=>"Zaoshi", "last_name"=>"Xu", "scopus_author_id"=>"55547725500"}, {"first_name"=>"Hanna", "last_name"=>"Lapko", "scopus_author_id"=>"36144345200"}, {"first_name"=>"Michael", "last_name"=>"Fromm", "scopus_author_id"=>"7102387020"}, {"first_name"=>"Zoya", "last_name"=>"Avramova", "scopus_author_id"=>"7003700704"}], "year"=>2012, "source"=>"PLoS Genetics", "identifiers"=>{"issn"=>"15537390", "scopus"=>"2-s2.0-84872027256", "sgr"=>"84872027256", "pui"=>"368067342", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "pmid"=>"23284292", "doi"=>"10.1371/journal.pgen.1003111"}, "id"=>"7ad14d1b-70f1-32bc-a0ff-c2a85c6a2121", "abstract"=>"Tri-methylated H3 lysine 4 (H3K4me3) is associated with transcriptionally active genes, but its function in the transcription process is still unclear. Point mutations in the catalytic domain of ATX1 (ARABIDOPSIS TRITHORAX1), a H3K4 methyltransferase, and RNAi knockdowns of subunits of the AtCOMPASS-like (Arabidopsis Complex Proteins Associated with Set) were used to address this question. We demonstrate that both ATX1 and AtCOMPASS-like are required for high level accumulation of TBP (TATA-binding protein) and Pol II at promoters and that this requirement is independent of the catalytic histone modifying activity. However, the catalytic function is critically required for transcription as H3K4me3 levels determine the efficiency of transcription elongation. The roles of H3K4me3, ATX1, and AtCOMPASS-like may be of a general relevance for transcription of Trithorax-activated eukaryotic genes.", "link"=>"http://www.mendeley.com/research/atx1generated-h3k4me3-required-efficient-elongation-transcription-not-initiation-atx1regulated-genes", "reader_count"=>69, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>20, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>2, "Student > Master"=>10, "Student > Bachelor"=>6, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>20, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>2, "Student > Master"=>10, "Student > Bachelor"=>6, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>13, "Agricultural and Biological Sciences"=>51, "Medicine and Dentistry"=>1, "Neuroscience"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>51}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Austria"=>1, "United States"=>1, "Portugal"=>1, "Germany"=>1}, "group_count"=>2}

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• {"files"=>["https://ndownloader.figshare.com/files/281950", "https://ndownloader.figshare.com/files/282007", "https://ndownloader.figshare.com/files/282066", "https://ndownloader.figshare.com/files/282137", "https://ndownloader.figshare.com/files/282176", "https://ndownloader.figshare.com/files/282225", "https://ndownloader.figshare.com/files/282286"], "description"=>"<div><p>Tri-methylated H3 lysine 4 (H3K4me3) is associated with transcriptionally active genes, but its function in the transcription process is still unclear. Point mutations in the catalytic domain of ATX1 (ARABIDOPSIS TRITHORAX1), a H3K4 methyltransferase, and RNAi knockdowns of subunits of the AtCOMPASS–like (Arabidopsis Complex Proteins Associated with Set) were used to address this question. We demonstrate that both ATX1 and AtCOMPASS–like are required for high level accumulation of TBP (TATA-binding protein) and Pol II at promoters and that this requirement is independent of the catalytic histone modifying activity. However, the catalytic function is critically required for transcription as H3K4me3 levels determine the efficiency of transcription elongation. The roles of H3K4me3, ATX1, and AtCOMPASS–like may be of a general relevance for transcription of Trithorax-activated eukaryotic genes.</p> </div>", "links"=>[], "tags"=>["atx1-generated", "h3k4me3", "elongation", "atx1-regulated", "genes"], "article_id"=>115592, "categories"=>["Biological Sciences"], "users"=>["Yong Ding", "Ivan Ndamukong", "Zaoshi Xu", "Hanna Lapko", "Michael Fromm", "Zoya Avramova"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003111.s001", "https://dx.doi.org/10.1371/journal.pgen.1003111.s002", "https://dx.doi.org/10.1371/journal.pgen.1003111.s003", "https://dx.doi.org/10.1371/journal.pgen.1003111.s004", "https://dx.doi.org/10.1371/journal.pgen.1003111.s005", "https://dx.doi.org/10.1371/journal.pgen.1003111.s006", "https://dx.doi.org/10.1371/journal.pgen.1003111.s007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/ATX1_Generated_H3K4me3_Is_Required_for_Efficient_Elongation_of_Transcription_Not_Initiation_at_ATX1_Regulated_Genes__/115592", "title"=>"ATX1-Generated H3K4me3 Is Required for Efficient Elongation of Transcription, Not Initiation, at ATX1-Regulated Genes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-12-20 01:33:12"}
• {"files"=>["https://ndownloader.figshare.com/files/519376"], "description"=>"<p>A) Relative H3K4me3 levels at <i>WRKY70</i> and <i>LTP7</i> in control wild type plants transformed with the empty vector (Con), in <i>AtWRD5-RNAi</i> (<i>w</i>R1, <i>w</i>R2) lines (top panels), <i>AtASH2-RNAi</i> (<i>a</i>R7, <i>a</i>R16) lines (middle panels), and <i>AtRbBp5a-RNAi</i> (<i>rb</i>R11, <i>rb</i>R14) lines (bottom panels) as measured by ChIP-PCR with HK4me3-specific antibodies. For characterization of the RNAi lines see SF 1A, B). Specific primers used for each gene are at the 5′-end, at the peak of H3K4me3 accumulation (Region 2, as indicated in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003111#pgen-1003111-g002\" target=\"_blank\">Figure 2A</a>). Background levels for immunoprecipitated samples with IgG as a control in all genetic backgrounds were <0.001 of the input levels (not shown). <i>ACT 7</i> is used as an internal control; B) Relative transcript levels produced by the genes in the RNAi knockdown lines described above. Each experiment was repeated at least three times. Each bar is standard errors of the mean (±SEMs, n = 3).</p>", "links"=>[], "tags"=>["mrna", "levels", "atx1-regulated", "genes", "at5-deficient"], "article_id"=>189866, "categories"=>["Biological Sciences"], "users"=>["Yong Ding", "Ivan Ndamukong", "Zaoshi Xu", "Hanna Lapko", "Michael Fromm", "Zoya Avramova"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003111.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_H3K4me3_and_mRNA_levels_of_two_ATX1_regulated_genes_in_the_AtWRD5_or_AtASH2_or_At5_deficient_lines_/189866", "title"=>"H3K4me3 and mRNA levels of two ATX1-regulated genes in the AtWRD5, or AtASH2, or At5-deficient lines.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 02:44:26"}
• {"files"=>["https://ndownloader.figshare.com/files/519515"], "description"=>"<p>A) Schematic diagram of the ATX1-regulated <i>WRKY70</i> and <i>LTP7</i> genes as well as the ATX1-independent <i>ACT7</i> gene. The 5′ or 3′ untranslated regions are shown as open boxes, the exons as black boxes, and the introns as thin black lines. Numbers below show the locations of the regions analyzed by ChIP-PCR; B) Distribution and amounts of AtWDR5 determined by ChIP-PCR with antibodies against WDR5 in WS (blue columns) and <i>atx1</i> (red columns) backgrounds; C) ChIP-PCR of WDR5, ATX1, and H3K4me3 in WS and AtWDR5 knockdown lines (<i>wR1,wR2</i>). Numbers on the X-axis show amplified regions as indicated in A. ChIP-PCR values with IgG in all genetic backgrounds were <0.001 of the input levels (not shown). Each experiment was repeated at least three times. Each bar is standard errors of the mean (±SEMs, n = 3).</p>", "links"=>[], "tags"=>["profiles", "h3k4me3", "atx1-regulated", "genes"], "article_id"=>190011, "categories"=>["Biological Sciences"], "users"=>["Yong Ding", "Ivan Ndamukong", "Zaoshi Xu", "Hanna Lapko", "Michael Fromm", "Zoya Avramova"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003111.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_profiles_of_AtWDR5_ATX1_and_H3K4me3_at_the_ATX1_regulated_genes_in_different_genotypes_/190011", "title"=>"Distribution profiles of AtWDR5, ATX1, and H3K4me3 at the ATX1-regulated genes in different genotypes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:00:11"}
• {"files"=>["https://ndownloader.figshare.com/files/519633"], "description"=>"<p>Transcription rates of the ATX1-regulated genes determined by nuclear run on assays in empty vector (Con), RNAi knockdown plants deficient for AtWDR5 (<i>w</i>R1 and <i>w</i>R2) or AtAsh2 (<i>a</i>2R7 and <i>a</i>2R16). Each experiment was repeated at least three times. Each bar is standard errors of the mean (±SEMs, n = 3).</p>", "links"=>[], "tags"=>["transcription", "rates", "atx1-regulated"], "article_id"=>190130, "categories"=>["Biological Sciences"], "users"=>["Yong Ding", "Ivan Ndamukong", "Zaoshi Xu", "Hanna Lapko", "Michael Fromm", "Zoya Avramova"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003111.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Role_of_AtCOMPASS_8211_like_in_the_transcription_rates_of_the_ATX1_regulated_genes_/190130", "title"=>"Role of AtCOMPASS–like in the transcription rates of the ATX1-regulated genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:02:10"}
• {"files"=>["https://ndownloader.figshare.com/files/519741"], "description"=>"<p>A) Relative TBP levels at the promoters of the <i>WRKY70</i> and <i>LTP7</i> genes in empty vector control (Con) plants, in <i>AtWRD5-RNAi</i> (<i>w</i>R1, <i>w</i>R2) lines (top panel) and the <i>AtASH2-RNAi</i> (<i>a2</i>R7, <i>a2</i>R16) lines (bottom panel). <i>ACT 7</i> is used as an internal control; B–C) total Pol II and Ser5P distribution profiles along the genes in control (Con) and RNAi knockdown genotypes as specified above. Amplified regions are numbered as indicated in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003111#pgen-1003111-g002\" target=\"_blank\">Figure 2A</a>. ChIP-PCR values with IgG in all genetic backgrounds were <0.001 of the input levels (not shown). Each experiment was repeated at least three times. Each bar is standard errors of the mean (±SEMs, n = 3).</p>", "links"=>[], "tags"=>["patterns", "levels", "rna", "pol", "ser5p"], "article_id"=>190227, "categories"=>["Biological Sciences"], "users"=>["Yong Ding", "Ivan Ndamukong", "Zaoshi Xu", "Hanna Lapko", "Michael Fromm", "Zoya Avramova"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003111.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_patterns_and_levels_of_TBP_of_total_RNA_Pol_II_and_of_Ser5P_Pol_II_/190227", "title"=>"Distribution patterns and levels of TBP, of total RNA Pol II, and of Ser5P Pol II.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:03:47"}
• {"files"=>["https://ndownloader.figshare.com/files/519868"], "description"=>"<p>Distribution of Ser2P Pol II along the three genes in empty vector control (Con), <i>AtWRD5-RNAi</i> (<i>w</i>R1, <i>w</i>R2) and <i>AtASH2-RNAi</i> (<i>a</i>R7 and <i>a</i>R16) lines. ChIP-PCR values with IgG in all genetic backgrounds were <0.001 of the input levels (not shown). Each experiment was repeated at least three times. Each bar is standard errors of the mean (±SEMs, n = 3).</p>", "links"=>[], "tags"=>["pol", "ii", "patterns", "genes", "knockdown"], "article_id"=>190355, "categories"=>["Biological Sciences"], "users"=>["Yong Ding", "Ivan Ndamukong", "Zaoshi Xu", "Hanna Lapko", "Michael Fromm", "Zoya Avramova"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003111.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ser2P_Pol_II_distribution_patterns_along_the_genes_in_AtWDR5_or_AtASH2_RNAi_knockdown_lines_/190355", "title"=>"Ser2P Pol II distribution patterns along the genes in <i>AtWDR5</i> or <i>AtASH2-RNAi</i> knockdown lines.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:05:55"}
• {"files"=>["https://ndownloader.figshare.com/files/519994"], "description"=>"<p>A) Transcript levels of <i>WRKY70</i> and <i>LTP7</i> genes in wild type (WS), two different <i>atx1:: ATX1-set</i> mutants (<i>setm1</i> and <i>setm2</i>, respectively; see SF 1), and <i>atx1</i> backgrounds; B) The amount of HA-tagged ATX1-set in the <i>atx1</i> background at the ATX1-regulated genes as determined by ChIP-PCR with antiHA antibody. Wild type (WS) was used as the non-specific control for the antiHA preciptiation as it lacks HA-tagged ATX1; C) Levels of H3K4me3 at the genes in wild type and the mutant backgrounds. Numbers on the x-coordinate represent regions along the gene sequences as indicated in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003111#pgen-1003111-g002\" target=\"_blank\">Figure 2A</a>, where specific primers were used in the ChIP-PCR assay. ChIP-PCR values with IgG in all genetic backgrounds were <0.001 of the input levels (not shown). Each experiment was repeated at least three times. Each bar is standard errors of the mean (±SEMs, n = 3).</p>", "links"=>[], "tags"=>["responses", "genes", "ha-tagged", "atx1-set", "h3k4me3"], "article_id"=>190486, "categories"=>["Biological Sciences"], "users"=>["Yong Ding", "Ivan Ndamukong", "Zaoshi Xu", "Hanna Lapko", "Michael Fromm", "Zoya Avramova"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003111.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transcriptional_responses_of_WRKY70_and_LTP7_genes_and_the_amount_of_HA_tagged_ATX1_set_and_H3K4me3_at_these_genes_in_different_backgrounds_/190486", "title"=>"Transcriptional responses of <i>WRKY70</i> and <i>LTP7</i> genes and the amount of HA-tagged ATX1-set and H3K4me3 at these genes in different backgrounds.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:08:06"}
• {"files"=>["https://ndownloader.figshare.com/files/520148"], "description"=>"<p>A) Occupancy by AtWDR5 at the promoters (region 1) and downstream regions; B) Distribution of Ser2P along the genes; C) Levels of TBP recruited to the promoters and D) of Ser5P Pol II at the promoters of the two genes in the different backgrounds. ChIP-PCR values with IgG in all genetic backgrounds were <0.001 of the input levels (not shown). Amplified regions are as indicated in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003111#pgen-1003111-g002\" target=\"_blank\">Figure 2A</a>). Each experiment was repeated at least three times. Each bar is standard errors of the mean (±SEMs, n = 3).</p>", "links"=>[], "tags"=>["ser2p", "pol", "ii"], "article_id"=>190634, "categories"=>["Biological Sciences"], "users"=>["Yong Ding", "Ivan Ndamukong", "Zaoshi Xu", "Hanna Lapko", "Michael Fromm", "Zoya Avramova"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003111.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Occupancy_of_WDR5_TBP_Ser5P_and_Ser2P_Pol_II_in_WS_atx1_or_atx1_ATX1_set_setm1_and_setm2_backgrounds_/190634", "title"=>"Occupancy of WDR5, TBP, Ser5P, and Ser2P Pol II in WS, atx1, or atx1::ATX1-set (setm1 and setm2) backgrounds.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:10:34"}
• {"files"=>["https://ndownloader.figshare.com/files/520249"], "description"=>"<p>A) The levels of PIC assembled at promoters depend on the integrity of ATX1/AtCOMPASS–like as ATX1 occurs in a complex with TBP (yellow) and interacts with the carboxyl terminal domain of Pol II (CTD, blue tail). The bar graph in A below the template shows the relative TBP levels that occur in wild type ATX1 (green), in the ATX1-setm mutant (Setm, in purple), in RNAi COMPASS-like knockdowns (blue), and in <i>atx1</i> (black) backgrounds; B) The transition to transcription initiation and promoter proximal pausing (gray pause rectangle) occurs with similar efficiencies (gray Pol II entry arrows of similar width) for both complexes that differ only in their ATX1 subunits: wild type ATX1 (top green ATX1) and ATX1-setm mutant (bottom purple Setm). Both wild type and the ATX1-setm ATX1/COMPASS-like complexes are recruited to this site via ATX1's affinity for the Ser5P form of Pol II. Wild type ATX1/COMPASS-like produce normal amounts of H3K4me3 levels, but H3K4me3 levels are diminished in the ATX1-setm mutant (the black line above the templates shows H3K4me3 profile). The levels of H3K4me3 affect the rate of Pol II exit from the promoter proximal pause region (size of gray Pol II exit arrows below the templates), with a higher exit rate for the wild type template. These different exit rates lead to more Pol II Ser2P complexes active in transcription elongation in ATX1 than in the ATX1-setm mutant.</p>", "links"=>[], "tags"=>["h3k4me3"], "article_id"=>190743, "categories"=>["Biological Sciences"], "users"=>["Yong Ding", "Ivan Ndamukong", "Zaoshi Xu", "Hanna Lapko", "Michael Fromm", "Zoya Avramova"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003111.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Model_for_the_roles_of_ATX1_AtCOMPASS_8211_like_and_H3K4me3_in_transcription_/190743", "title"=>"Model for the roles of ATX1/AtCOMPASS–like and H3K4me3 in transcription.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:12:23"}
• {"files"=>["https://ndownloader.figshare.com/files/520353"], "description"=>"1<p>The average of the ChIP-PCR values ± SD, n = 4, for w<i>dr5R1</i>, <i>wdr5R2</i>, <i>ash2R7</i>, and <i>ash2R16 RNAi</i> knockdown lines, as a percent of wild type. The 5′ and 3′-end regions correspond to regions 2 and 6 in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003111#pgen-1003111-g002\" target=\"_blank\">Figure 2</a>; for the shorter <i>LTP7</i> gene the 3′ end corresponds to region 3. <i>P</i>-values are for the significance of the differences between the 5′-end and 3′-ends.</p>", "links"=>[], "tags"=>["pol", "ii", "phosphorylated", "forms", "rnai", "compass", "subunit-knockdown"], "article_id"=>190839, "categories"=>["Biological Sciences"], "users"=>["Yong Ding", "Ivan Ndamukong", "Zaoshi Xu", "Hanna Lapko", "Michael Fromm", "Zoya Avramova"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003111.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_total_Pol_II_or_its_phosphorylated_forms_in_RNAi_COMPASS_subunit_knockdown_lines_/190839", "title"=>"Distribution of total Pol II or its phosphorylated forms in RNAi COMPASS subunit-knockdown lines.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-12-20 00:13:59"}

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Relative Metric

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F1000Prime