Structural Basis of Transcriptional Gene Silencing Mediated by Arabidopsis MOM1
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{"title"=>"Structural basis of transcriptional gene silencing mediated by Arabidopsis MOM1", "type"=>"journal", "authors"=>[{"first_name"=>"Taisuke", "last_name"=>"Nishimura", "scopus_author_id"=>"13005587700"}, {"first_name"=>"Guillaume", "last_name"=>"Molinard", "scopus_author_id"=>"55159661600"}, {"first_name"=>"Tom J.", "last_name"=>"Petty", "scopus_author_id"=>"57197301111"}, {"first_name"=>"Larissa", "last_name"=>"Broger", "scopus_author_id"=>"16641914200"}, {"first_name"=>"Caroline", "last_name"=>"Gabus", "scopus_author_id"=>"6603901559"}, {"first_name"=>"Thanos D.", "last_name"=>"Halazonetis", "scopus_author_id"=>"7005983275"}, {"first_name"=>"Stéphane", "last_name"=>"Thore", "scopus_author_id"=>"6701640615"}, {"first_name"=>"Jerzy", "last_name"=>"Paszkowski", "scopus_author_id"=>"7003688720"}], "year"=>2012, "source"=>"PLoS Genetics", "identifiers"=>{"pmid"=>"22346760", "doi"=>"10.1371/journal.pgen.1002484", "sgr"=>"84859196351", "isbn"=>"1553-7390", "scopus"=>"2-s2.0-84859196351", "issn"=>"15537390", "pui"=>"364547157"}, "id"=>"83099219-5e0a-3939-b51c-e7b60bdd6ea2", "abstract"=>"Shifts between epigenetic states of transcriptional activity are typically correlated with changes in epigenetic marks. However, exceptions to this rule suggest the existence of additional, as yet uncharacterized, layers of epigenetic regulation. MOM1, a protein of 2,001 amino acids that acts as a transcriptional silencer, represents such an exception. Here we define the 82 amino acid domain called CMM2 (Conserved MOM1 Motif 2) as a minimal MOM1 fragment capable of transcriptional regulation. As determined by X-ray crystallography, this motif folds into an unusual hendecad-based coiled-coil. Structure-based mutagenesis followed by transgenic complementation tests in plants demonstrate that CMM2 and its dimerization are effective for transcriptional suppression at chromosomal loci co-regulated by MOM1 and the siRNA pathway but not at loci controlled by MOM1 in an siRNA-independent fashion. These results reveal a surprising separation of epigenetic activities that enable the single, large MOM1 protein to coordinate cooperating mechanisms of epigenetic regulation.", "link"=>"http://www.mendeley.com/research/structural-basis-transcriptional-gene-silencing-mediated-arabidopsis-mom1", "reader_count"=>59, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>11, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>4, "Other"=>5, "Student > Master"=>9, "Student > Bachelor"=>5, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>11, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>4, "Other"=>5, "Student > Master"=>9, "Student > Bachelor"=>5, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>46, "Medicine and Dentistry"=>1, "Neuroscience"=>1, "Chemistry"=>1, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>46}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Czech Republic"=>1, "Austria"=>1, "United States"=>2, "United Kingdom"=>1, "France"=>1}, "group_count"=>3}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/684241"], "description"=>"<p>(A) <i>Left</i>, schematic models of transgene constructs used for transgenic complementation assays in <i>mom1</i> L5 plants. “X” represents mutations colored as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002484#pgen-1002484-g003\" target=\"_blank\">Figure 3</a>. <i>Right</i>, histochemical GUS staining of cotyledons of eight independent 1-week-old T1 transgenic plants transformed with the corresponding mutant derivatives of miniMOM1. The “empty vector” control corresponds to <i>mom1</i> L5 transformed with a vector construct without miniMOM1. (B) Relative levels of <i>GUS</i> mRNA in T2 plants from 3 independent T1 plants determined by quantitative RT-PCR and normalized to 18S rRNA. The mean of the “empty vector” control was set to 1. Error bars represent S.E. calculated from 3 experimental sets of 40 to 50 plants each.</p>", "links"=>[], "tags"=>["cmm2", "domains", "tgs"], "article_id"=>354727, "categories"=>["Biochemistry", "Genetics"], "users"=>["Taisuke Nishimura", "Guillaume Molinard", "Tom J. Petty", "Larissa Broger", "Caroline Gabus", "Thanos D. Halazonetis", "Stéphane Thore", "Jerzy Paszkowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002484.g004", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multimerization_of_CMM2_domains_are_crucial_for_TGS_activity_/354727", "title"=>"Multimerization of CMM2 domains are crucial for TGS activity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:18:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/684372"], "description"=>"<p>Relative levels of mRNAs in T2 plants of various MOM1 target loci determined by quantitative RT-PCR and normalized to 18S rRNA. The targets regulated by MOM1 co-operatively with RdDM (A) and largely by MOM1 only (B) were investigated. These T2 plants were delivered from 3 independent T1 plants. The mean of “empty vector in <i>mom1</i>” was set to 1. The mean values of relative expression are indicated above columns. Error bars represent S.E. calculated from 3 experimental sets of 40 to 50 plants each.</p>", "links"=>[], "tags"=>["acts", "selectively", "mom1-regulated", "tgs"], "article_id"=>354854, "categories"=>["Biochemistry", "Genetics"], "users"=>["Taisuke Nishimura", "Guillaume Molinard", "Tom J. Petty", "Larissa Broger", "Caroline Gabus", "Thanos D. Halazonetis", "Stéphane Thore", "Jerzy Paszkowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002484.g005", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CMM2_acts_selectively_on_MOM1_regulated_TGS_targets_/354854", "title"=>"CMM2 acts selectively on MOM1-regulated TGS targets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:20:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/684124"], "description"=>"<p>(A) Radial net representation of the CMM2 sequence with the mutated amino acids of the CMM2-mut1, -mut2 and -mut3 constructs indicated in red, yellow and orange, respectively. On each side of the radial net, the CMM2 coiled-coil structure is shown as green- and orange ribbons with the targeted amino acids displayed as sticks surrounded with a mesh surface (colored as described above). (B) Schematic presentation of vectors used in the yeast two-hybrid experiments (<i>left</i>) and α-galactosidase staining of yeast co-transformed with corresponding protein fusions (right). “X” on the construct models represents approximate positions of mutations (colored according to A). The “empty vector” contained only GAL4-AD and GAL4-BD.</p>", "links"=>[], "tags"=>["cmm2", "domains"], "article_id"=>354612, "categories"=>["Biochemistry", "Genetics"], "users"=>["Taisuke Nishimura", "Guillaume Molinard", "Tom J. Petty", "Larissa Broger", "Caroline Gabus", "Thanos D. Halazonetis", "Stéphane Thore", "Jerzy Paszkowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002484.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Intermolecular_interaction_of_CMM2_domains_in_vivo_/354612", "title"=>"Intermolecular interaction of CMM2 domains <i>in vivo.</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:16:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/683826"], "description"=>"<p>(A) Schematic representation for MOM1 and miniMOM1. (B) <i>Left</i>, deletion derivatives of miniMOM1 that were introduced to <i>mom1</i> L5 plants harboring a transgenic L5 locus encoding ß-glucuronidase <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002484#pgen.1002484-Morel1\" target=\"_blank\">[25]</a>. <i>Right</i>, histochemical GUS staining of cotyledons of seven independent 1-week-old T1 transgenic plants transformed with the corresponding miniMOM1 deletion derivatives. The “empty vector” control corresponds to <i>mom1</i> L5 transformed with a vector construct without miniMOM1 sequences. (C) Relative levels of <i>GUS</i> mRNA in T2 plants from 3 independent T1 plants determined by quantitative RT-PCR and normalized to 18S rRNA. The mean of the “empty vector” control was set to 1. Error bars represent S.E. calculated from 3 experimental sets of 40 to 50 plants each.</p>", "links"=>[], "tags"=>["tgs"], "article_id"=>354306, "categories"=>["Biochemistry", "Genetics"], "users"=>["Taisuke Nishimura", "Guillaume Molinard", "Tom J. Petty", "Larissa Broger", "Caroline Gabus", "Thanos D. Halazonetis", "Stéphane Thore", "Jerzy Paszkowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002484.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CMM2_is_necessary_and_sufficient_for_the_TGS_activity_of_MOM1_/354306", "title"=>"CMM2 is necessary and sufficient for the TGS activity of MOM1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:11:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/348634", "https://ndownloader.figshare.com/files/348689", "https://ndownloader.figshare.com/files/348723", "https://ndownloader.figshare.com/files/348758", "https://ndownloader.figshare.com/files/348839", "https://ndownloader.figshare.com/files/348903"], "description"=>"<div><p>Shifts between epigenetic states of transcriptional activity are typically correlated with changes in epigenetic marks. However, exceptions to this rule suggest the existence of additional, as yet uncharacterized, layers of epigenetic regulation. MOM1, a protein of 2,001 amino acids that acts as a transcriptional silencer, represents such an exception. Here we define the 82 amino acid domain called CMM2 (Conserved MOM1 Motif 2) as a minimal MOM1 fragment capable of transcriptional regulation. As determined by X-ray crystallography, this motif folds into an unusual hendecad-based coiled-coil. Structure-based mutagenesis followed by transgenic complementation tests in plants demonstrate that CMM2 and its dimerization are effective for transcriptional suppression at chromosomal loci co-regulated by MOM1 and the siRNA pathway but not at loci controlled by MOM1 in an siRNA–independent fashion. These results reveal a surprising separation of epigenetic activities that enable the single, large MOM1 protein to coordinate cooperating mechanisms of epigenetic regulation.</p> </div>", "links"=>[], "tags"=>["transcriptional", "mediated", "mom1"], "article_id"=>128930, "categories"=>["Biochemistry", "Genetics"], "users"=>["Taisuke Nishimura", "Guillaume Molinard", "Tom J. Petty", "Larissa Broger", "Caroline Gabus", "Thanos D. Halazonetis", "Stéphane Thore", "Jerzy Paszkowski"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002484.s001", "https://dx.doi.org/10.1371/journal.pgen.1002484.s002", "https://dx.doi.org/10.1371/journal.pgen.1002484.s003", "https://dx.doi.org/10.1371/journal.pgen.1002484.s004", "https://dx.doi.org/10.1371/journal.pgen.1002484.s005", "https://dx.doi.org/10.1371/journal.pgen.1002484.s006"], "stats"=>{"downloads"=>9, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Structural_Basis_of_Transcriptional_Gene_Silencing_Mediated_by_Arabidopsis_MOM1/128930", "title"=>"Structural Basis of Transcriptional Gene Silencing Mediated by <em>Arabidopsis</em> MOM1", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-02-09 02:28:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/683970"], "description"=>"<p>(A) Overall view of the CMM2 coiled-coil structure. The two monomers are depicted as orange- and green-colored ribbons and the residues forming the interface are shown using the stick representation and colored in blue. (B) Sequence alignment of the different CMM2 sequences found in plants <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002484#pgen.1002484-aikovski1\" target=\"_blank\">[24]</a>. At - <i>Arabidopsis thaliana</i>, Pt - <i>Populus trichocarpa</i>, Vv - <i>Vitis vinifera</i>, Os - <i>Oryza sativa</i>, Pta - <i>Pinus taeda</i>, Zm - <i>Zea mays</i>, Ac - <i>Aquilegia coerulea</i>, Mt - <i>Medicago truncatula</i>, Sm - <i>Selaginella moellendorffii.</i> The hydrophobic residues forming the interphase are highlighted in blue (shown in A). The repeated pattern of amino acids is indicated in letters referring to their positions. Heptad repeats are underlined and hendecad's repeats are in bold. (C) Axial view of the CMM2 monomer structure together with the radial net showing the position of each amino acid on a flat surface. The vertical bars on the right side represent change in the α-helical axis direction. The N-terminus is at the bottom and the C-terminus on top. Amino acids at position A, D and H are highlighted in blue. (D) Hydrophobic interface formed by the tips of the CMM2 monomers. Symmetry-related CMM2 monomers are depicted as orange- and green-colored ribbons. Amino acids involved in the interaction are show as sticks and colored according to their atom types (carbon: white, nitrogen: blue, oxygen, red). (E) View of the intra- and intermolecular salt bridges stabilizing the CMM2 coiled-coil. Amino acids are labeled and depicted as in panel D. Hydrogen bonds are shown as dashed lines. (F) View along the axis of the CMM2 helices illustrating the difference between the orientation of amino acids in positions e or i and in positions k or g. (G) Schematic representation of the amino acid positions in the CMM2 anti-parallel coiled-coil structure. Positions forming the hydrophobic interface are in capital letters. Images were prepared with the program PyMOL (W.L. Delano, The PyMOL Molecular Graphics System, DeLano Scientific, Palo Alto, CA (2002)).</p>", "links"=>[], "tags"=>["cmm2"], "article_id"=>354455, "categories"=>["Biochemistry", "Genetics"], "users"=>["Taisuke Nishimura", "Guillaume Molinard", "Tom J. Petty", "Larissa Broger", "Caroline Gabus", "Thanos D. Halazonetis", "Stéphane Thore", "Jerzy Paszkowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002484.g002", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Crystal_structure_of_the_CMM2_protein_fragment_/354455", "title"=>"Crystal structure of the CMM2 protein fragment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:14:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/684490"], "description"=>"<p>Relative levels of mRNAs in T2 plants of various MOM1 target loci determined by quantitative RT-PCR and normalized to 18S rRNA. These T2 plants were delivered from 3 independent T1 plants. The mean of “empty vector in <i>mom1</i>” was set to 1. Error bars represent S.E. calculated from 3 experimental sets of 40 to 50 plants each.</p>", "links"=>[], "tags"=>["cmm2", "domains", "tgs", "chromosomal"], "article_id"=>354975, "categories"=>["Biochemistry", "Genetics"], "users"=>["Taisuke Nishimura", "Guillaume Molinard", "Tom J. Petty", "Larissa Broger", "Caroline Gabus", "Thanos D. Halazonetis", "Stéphane Thore", "Jerzy Paszkowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002484.g006", "stats"=>{"downloads"=>3, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multimerization_of_CMM2_domains_is_crucial_for_TGS_activity_at_various_chromosomal_loci_/354975", "title"=>"Multimerization of CMM2 domains is crucial for TGS activity at various chromosomal loci.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:22:55"}

PMC Usage Stats | Further Information

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  • {"month"=>"6", "scanned-page-browse"=>"0", "cited-by"=>"0", "abstract"=>"0", "full-text"=>"22", "year"=>"2012", "pdf"=>"9", "unique-ip"=>"23", "figure"=>"13", "scanned-summary"=>"0", "supp-data"=>"1"}
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  • {"unique-ip"=>"25", "full-text"=>"18", "pdf"=>"10", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2012", "month"=>"10"}
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  • {"unique-ip"=>"12", "full-text"=>"9", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2013", "month"=>"4"}
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  • {"unique-ip"=>"18", "full-text"=>"8", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"10"}
  • {"unique-ip"=>"6", "full-text"=>"9", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"11"}
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  • {"unique-ip"=>"11", "full-text"=>"9", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2015", "month"=>"2"}
  • {"unique-ip"=>"13", "full-text"=>"13", "pdf"=>"17", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2015", "month"=>"3"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"25", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"4"}
  • {"unique-ip"=>"13", "full-text"=>"13", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"5"}
  • {"unique-ip"=>"2", "full-text"=>"5", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"6"}
  • {"unique-ip"=>"14", "full-text"=>"12", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"7"}
  • {"unique-ip"=>"8", "full-text"=>"4", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"8"}
  • {"unique-ip"=>"9", "full-text"=>"8", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"9"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"10"}
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Relative Metric

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