Raf1 Is a DCAF for the Rik1 DDB1-Like Protein and Has Separable Roles in siRNA Generation and Chromatin Modification
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{"title"=>"Raf1 is a DCAF for the Rik1 DDB1-like protein and has separable roles in siRNA generation and chromatin modification", "type"=>"journal", "authors"=>[{"first_name"=>"Alessia", "last_name"=>"Buscaino", "scopus_author_id"=>"8934363000"}, {"first_name"=>"Sharon A.", "last_name"=>"White", "scopus_author_id"=>"55338854200"}, {"first_name"=>"Douglas R.", "last_name"=>"Houston", "scopus_author_id"=>"7102073205"}, {"first_name"=>"Erwan", "last_name"=>"Lejeune", "scopus_author_id"=>"11339771300"}, {"first_name"=>"Femke", "last_name"=>"Simmer", "scopus_author_id"=>"6507984891"}, {"first_name"=>"Flavia", "last_name"=>"de Lima Alves", "scopus_author_id"=>"15845177300"}, {"first_name"=>"Piyush T.", "last_name"=>"Diyora", "scopus_author_id"=>"55159701100"}, {"first_name"=>"Takeshi", "last_name"=>"Urano", "scopus_author_id"=>"7201420574"}, {"first_name"=>"Elizabeth H.", "last_name"=>"Bayne", "scopus_author_id"=>"12773861100"}, {"first_name"=>"Juri", "last_name"=>"Rappsilber", "scopus_author_id"=>"6603851819"}, {"first_name"=>"Robin C.", "last_name"=>"Allshire", "scopus_author_id"=>"7004529628"}], "year"=>2012, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"84859166140", "scopus"=>"2-s2.0-84859166140", "doi"=>"10.1371/journal.pgen.1002499", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "pui"=>"364547175", "issn"=>"15537390", "pmid"=>"22319459"}, "id"=>"9679f2ce-024a-3dd2-8eb8-38c0760114ec", "abstract"=>"Non-coding transcription can trigger histone post-translational modifications forming specialized chromatin. In fission yeast, heterochromatin formation requires RNAi and the histone H3K9 methyltransferase complex CLRC, composed of Clr4, Raf1, Raf2, Cul4, and Rik1. CLRC mediates H3K9 methylation and siRNA production; it also displays E3-ubiquitin ligase activity in vitro. DCAFs act as substrate receptors for E3 ligases and may couple ubiquitination with histone methylation. Here, structural alignment and mutation of signature WDxR motifs in Raf1 indicate that it is a DCAF for CLRC. We demonstrate that Raf1 promotes H3K9 methylation and siRNA amplification via two distinct, separable functions. The association of the DCAF Raf1 with Cul4-Rik1 is critical for H3K9 methylation, but dispensable for processing of centromeric transcripts into siRNAs. Thus the association of a DCAF, Raf1, with its adaptor, Rik1, is required for histone methylation and to allow RNAi to signal to chromatin.", "link"=>"http://www.mendeley.com/research/raf1-dcaf-rik1-ddb1like-protein-separable-roles-sirna-generation-chromatin-modification", "reader_count"=>51, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>17, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>19, "Student > Master"=>6, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>17, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>19, "Student > Master"=>6, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>9, "Agricultural and Biological Sciences"=>39, "Business, Management and Accounting"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>39}, "Computer Science"=>{"Computer Science"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}}, "reader_count_by_country"=>{"United Kingdom"=>4}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/686801"], "description"=>"<p>(A) Yeast two-hybrid assay. Interaction of Raf1 with Rik1 is indicated by growth on -Leu, -Trp, -His, -Ade plates. BD and AD: GAL4 <i>B</i>inding or <i>A</i>ctivation <i>D</i>omain fusions, respectively. (B) Western of FLAG-Raf1, FLAG-Raf1-R518A FLAG-Raf1-R576A and FLAG-Raf1-1 IPs analysed for FLAG-Raf1 and Rik1-Myc (right: cells grown at 36°C). (C) Western of FLAG-Raf1, FLAG-Raf1-R518A FLAG-Raf1-R576A and FLAG-Raf1-1 IPs analysed for FLAG-Raf1 and Clr4-Myc (right: cells grown at 36°C). (D) FLAG-Raf1, FLAG-Raf1-R518A, FLAG-Raf1-R576A and FLAG-Raf1-1 ChIP. Diagram shows <i>cen1</i> primers used (black bar). Enrichment of FLAG-tagged proteins or untagged control were analysed by qPCR of <i>otr</i> relative to <i>act1</i><sup>+</sup>(bottom: cells grown at 36°C). Error bar SD. (E) Westerns of Raf2-TAP IP analysed for FLAG-Raf1, FLAG-Raf1-1, FLAG-Raf1-R518A and FLAG-Raf1-R576A (right: cells grown at 36°C).</p>", "links"=>[], "tags"=>["mutations", "disrupt"], "article_id"=>357280, "categories"=>["Cell Biology", "Genetics"], "users"=>["Alessia Buscaino", "Sharon A. White", "Douglas R. Houston", "Erwan Lejeune", "Femke Simmer", "Flavia de Lima Alves", "Piyush T. Diyora", "Takeshi Urano", "Elizabeth H. Bayne", "Juri Rappsilber", "Robin C. Allshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002499.g005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Raf1_mutations_disrupt_interaction_with_Rik1_/357280", "title"=>"Raf1 mutations disrupt interaction with Rik1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-02 02:01:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/686541"], "description"=>"<p>(A) <i>cen1:ade6</i><sup>+</sup> silencing assay in wt, <i>clr4Δ</i> or <i>raf1-1</i> cells at 25°, 32° or 36°C. (B) Percentage of lagging chromosomes in anaphase of wt, <i>raf1Δ</i> and <i>raf1-1</i> cells at 25°C or 36°C. Cell lacking heterochromatin display higher rates of chromosome missegregation at lower temperature <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002499#pgen.1002499-Ekwall1\" target=\"_blank\">[42]</a>. (C) H3K9me2 ChIP: levels associated with <i>cen-dg</i> relative to <i>act1</i><sup>+</sup> in <i>clr4Δ</i> and <i>raf1-1</i> cells normalised to wild-type at 25° or 36°C. Error bars: SD.</p>", "links"=>[], "tags"=>["conditionally", "disrupts"], "article_id"=>357022, "categories"=>["Cell Biology", "Genetics"], "users"=>["Alessia Buscaino", "Sharon A. White", "Douglas R. Houston", "Erwan Lejeune", "Femke Simmer", "Flavia de Lima Alves", "Piyush T. Diyora", "Takeshi Urano", "Elizabeth H. Bayne", "Juri Rappsilber", "Robin C. Allshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002499.g003", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_raf1_1_conditionally_disrupts_heterochromatin_/357022", "title"=>"<i>raf1-1</i> conditionally disrupts heterochromatin.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-02 01:57:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/686426"], "description"=>"<p>(A) Structural alignment of Raf1 (blue) with human DCAF DDB2 (grey). (B) Structural model of Rik1 (based on DDB1: grey) associated with Raf1 (red, green and yellow). In Raf1, the N-terminal helix (red) and the β-propeller (green and yellow) make specific interaction with Rik1. (C) Centromere silencing assay. Position of <i>ade6</i><sup>+</sup> marker gene in <i>cen1</i>. Wild-type cells with silenced <i>cen1:ade6</i><sup>+</sup> form red colonies; loss of silencing causes white colonies. (D) Lagging chromosomes in anaphase. Representative images of fixed cells stained with DAPI (red) and anti-tubulin (green) and % anaphase cells with lagging chromosomes. (E) H3K9me2 ChIP; levels associated with <i>cen-dg</i> relative to <i>act1</i><sup>+</sup>, normalised to wild-type. Error bars: standard deviation (SD). (F) Northern: unprocessed <i>otr</i> transcripts (arrows) in wt, <i>clr4Δ</i>, <i>raf1-R518A</i> and <i>raf1-R576A</i> cells. Loading control: rRNA. (*): rRNA background. (G) Northern: centromeric siRNAs in wt, <i>clr4Δ</i>, <i>raf1-R518A</i> and <i>raf1-R576A</i> cells. Loading control: snoRNA58.</p>", "links"=>[], "tags"=>["dcaf", "clrc", "wdxr", "motifs", "heterochromatin"], "article_id"=>356902, "categories"=>["Cell Biology", "Genetics"], "users"=>["Alessia Buscaino", "Sharon A. White", "Douglas R. Houston", "Erwan Lejeune", "Femke Simmer", "Flavia de Lima Alves", "Piyush T. Diyora", "Takeshi Urano", "Elizabeth H. Bayne", "Juri Rappsilber", "Robin C. Allshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002499.g002", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Raf1_is_the_DCAF_for_CLRC_with_WDxR_motifs_essential_for_heterochromatin_formation_/356902", "title"=>"Raf1 is the DCAF for CLRC with WDxR motifs essential for heterochromatin formation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-02 01:55:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/349997", "https://ndownloader.figshare.com/files/350042", "https://ndownloader.figshare.com/files/350093", "https://ndownloader.figshare.com/files/350166", "https://ndownloader.figshare.com/files/350196", "https://ndownloader.figshare.com/files/350222", "https://ndownloader.figshare.com/files/350274", "https://ndownloader.figshare.com/files/350298"], "description"=>"<div><p>Non-coding transcription can trigger histone post-translational modifications forming specialized chromatin. In fission yeast, heterochromatin formation requires RNAi and the histone H3K9 methyltransferase complex CLRC, composed of Clr4, Raf1, Raf2, Cul4, and Rik1. CLRC mediates H3K9 methylation and siRNA production; it also displays E3-ubiquitin ligase activity <em>in vitro</em>. DCAFs act as substrate receptors for E3 ligases and may couple ubiquitination with histone methylation. Here, structural alignment and mutation of signature WDxR motifs in Raf1 indicate that it is a DCAF for CLRC. We demonstrate that Raf1 promotes H3K9 methylation and siRNA amplification via two distinct, separable functions. The association of the DCAF Raf1 with Cul4-Rik1 is critical for H3K9 methylation, but dispensable for processing of centromeric transcripts into siRNAs. Thus the association of a DCAF, Raf1, with its adaptor, Rik1, is required for histone methylation and to allow RNAi to signal to chromatin.</p> </div>", "links"=>[], "tags"=>["raf1", "dcaf", "rik1", "ddb1-like", "separable", "roles", "sirna", "chromatin", "modification"], "article_id"=>129187, "categories"=>["Cell Biology", "Genetics"], "users"=>["Alessia Buscaino", "Sharon A. White", "Douglas R. Houston", "Erwan Lejeune", "Femke Simmer", "Flavia de Lima Alves", "Piyush T. Diyora", "Takeshi Urano", "Elizabeth H. Bayne", "Juri Rappsilber", "Robin C. Allshire"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002499.s001", "https://dx.doi.org/10.1371/journal.pgen.1002499.s002", "https://dx.doi.org/10.1371/journal.pgen.1002499.s003", "https://dx.doi.org/10.1371/journal.pgen.1002499.s004", "https://dx.doi.org/10.1371/journal.pgen.1002499.s005", "https://dx.doi.org/10.1371/journal.pgen.1002499.s006", "https://dx.doi.org/10.1371/journal.pgen.1002499.s007", "https://dx.doi.org/10.1371/journal.pgen.1002499.s008"], "stats"=>{"downloads"=>37, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Raf1_Is_a_DCAF_for_the_Rik1_DDB1_Like_Protein_and_Has_Separable_Roles_in_siRNA_Generation_and_Chromatin_Modification/129187", "title"=>"Raf1 Is a DCAF for the Rik1 DDB1-Like Protein and Has Separable Roles in siRNA Generation and Chromatin Modification", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-02-02 02:33:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/686920"], "description"=>"<p>(A) Top panel: The CLRC complex is an active E3 ligase. The DCAF Raf1 binds a specific substrate (X) allowing its ubiquitination. This is essential for methylation of H3K9. Bottom panel: The CLRC complex is not an active E3 ligase. Cul4, Rik1, Raf1 and Raf2 form a protein scaffold allowing the correct targeting of the histone methyltransferase Clr4. (B) Individual CLRC components stimulate processing of centromeric transcripts into siRNAs independently of CLRC complex integrity. Raf1-Raf2, methylation of Mlo3 or other substrates and Rik1 (left) are required for processing centromeric transcripts into siRNAs.</p>", "links"=>[], "tags"=>["clrc", "couples", "h3k9me", "sirna"], "article_id"=>357396, "categories"=>["Cell Biology", "Genetics"], "users"=>["Alessia Buscaino", "Sharon A. White", "Douglas R. Houston", "Erwan Lejeune", "Femke Simmer", "Flavia de Lima Alves", "Piyush T. Diyora", "Takeshi Urano", "Elizabeth H. Bayne", "Juri Rappsilber", "Robin C. Allshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002499.g006", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_CLRC_complex_couples_H3K9me_and_siRNA_production_/357396", "title"=>"The CLRC complex couples H3K9me and siRNA production.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-02 02:03:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/686302"], "description"=>"<p>(A) Immunolocalisation of GFP-Raf1 (top panel) or untagged control (bottom panel) localisation. Representative images of fixed cells: GFP-Raf1 (green), centromere specific protein CENP-A<sup>Cnp1</sup> (red), DAPI stained DNA (blue). (B) FLAG-Raf1 ChIP. Diagram shows position of <i>cen1</i> primers used (black bar). FLAG-Raf1 or untagged controls cells were analysed by multiplex PCR (<i>otr</i> enrichment relative to <i>fbp1<sup>+</sup></i> control - left) or by qPCR (<i>otr</i> enrichment relative to <i>act1</i><sup>+</sup> - right). I: input; IP: immunoprecipitation. (C) Proteins reproducibly detected in FLAG-Raf1 IPs by LC-MS/MS. Average peptide numbers identified in replicas is shown. (D) Raf1-FLAG IP analysed with anti-FLAG or with anti-Myc to detect Rik1-Myc.</p>", "links"=>[], "tags"=>["chromatin-associated", "clrc"], "article_id"=>356779, "categories"=>["Cell Biology", "Genetics"], "users"=>["Alessia Buscaino", "Sharon A. White", "Douglas R. Houston", "Erwan Lejeune", "Femke Simmer", "Flavia de Lima Alves", "Piyush T. Diyora", "Takeshi Urano", "Elizabeth H. Bayne", "Juri Rappsilber", "Robin C. Allshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002499.g001", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Raf1_is_a_chromatin_associated_CLRC_component_/356779", "title"=>"Raf1 is a chromatin-associated CLRC component.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-02 01:52:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/686659"], "description"=>"<p>(A) Swi6 localisation in indicated cells at 25° or 36°C. Representative images of fixed cells with Swi6 (green) and CENP-A<sup>Cnp1</sup>(red). % cells with Swi6 localised at centromeres. (B) Northern: unprocessed <i>otr</i> transcripts in indicated cells at 25° or 36°C. Loading control: rRNA. (C) <i>mat3-M:ura4</i><sup>+</sup> silencing assay of cells grown at 36°C and shifted to 25°C (top panel) or kept at 36°C (bottom panel). non-selective (N/S), –URA or 5-FOA plates indicated. Silencing (wt, <i>dcr1Δ</i> and <i>raf1-1</i> at 25°C) allows little growth on -URA but good growth on 5-FOA. Loss of silencing (<i>rik1Δ</i>, <i>raf1-1</i> at 36°C and <i>raf1-1 dcr1Δ</i> at 25° or 36°C) results in good growth on –URA and 5-FOA sensitivity. (D) Northern: centromeric siRNA in indicated cells at 25° or 36°C. Loading control: snoRNA58. (E) Northern: FLAG-Ago1-associated siRNA from indicated cells at 25° or 36°C.</p>", "links"=>[], "tags"=>["sirna", "erased"], "article_id"=>357138, "categories"=>["Cell Biology", "Genetics"], "users"=>["Alessia Buscaino", "Sharon A. White", "Douglas R. Houston", "Erwan Lejeune", "Femke Simmer", "Flavia de Lima Alves", "Piyush T. Diyora", "Takeshi Urano", "Elizabeth H. Bayne", "Juri Rappsilber", "Robin C. Allshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002499.g004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heterochromatin_but_not_siRNA_production_is_erased_in_raf1_1_cells_/357138", "title"=>"Heterochromatin, but not siRNA production, is erased in <i>raf1-1</i> cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-02 01:58:58"}

PMC Usage Stats | Further Information

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Relative Metric

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