Structure of Metaphase Chromosomes: A Role for Effects of Macromolecular Crowding
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{"title"=>"Structure of metaphase chromosomes: A role for effects of macromolecular crowding", "type"=>"journal", "authors"=>[{"first_name"=>"Ronald", "last_name"=>"Hancock", "scopus_author_id"=>"55439524900"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84859997953", "doi"=>"10.1371/journal.pone.0036045", "issn"=>"19326203", "pui"=>"364662487", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"22540018", "scopus"=>"2-s2.0-84859997953"}, "id"=>"d9ac4f35-edfe-3992-800a-b0ecb432ee44", "abstract"=>"In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ~30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100-200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll) in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ~30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes.", "link"=>"http://www.mendeley.com/research/structure-metaphase-chromosomes-role-effects-macromolecular-crowding", "reader_count"=>43, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>11, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>9, "Student > Master"=>6, "Student > Bachelor"=>10, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>11, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>9, "Student > Master"=>6, "Student > Bachelor"=>10, "Professor"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>30, "Medicine and Dentistry"=>2, "Physics and Astronomy"=>3, "Chemistry"=>3, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>3}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>30}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}}, "reader_count_by_country"=>{"Netherlands"=>2, "United States"=>2, "France"=>1, "Germany"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/649367"], "description"=>"<p>Sections are approximately longitudinal or transversal in (A) and (B), respectively. (C) Chromatin fibres in regions of lower density at the periphery of chromosomes; white arrows illustrate regions where fibres of ∼30 nm diameter are seen. Scale bars (A, B), 1 µm; (C), 30 nm.</p>", "links"=>[], "tags"=>["electron", "microscopy", "chromosomes", "released"], "article_id"=>319864, "categories"=>["Physics", "Biochemistry", "Cell Biology", "Genetics", "Biophysics"], "users"=>["Ronald Hancock"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036045.g002", "stats"=>{"downloads"=>0, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Images_by_transmission_electron_microscopy_of_chromosomes_released_in_12_PEG_/319864", "title"=>"Images by transmission electron microscopy of chromosomes released in 12% PEG.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 06:08:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/649503"], "description"=>"<p>Chromosomes released in 12% PEG were deposited on slides and incubated for 1 h with PEG at the concentration shown in 100 µm K-Hepes buffer, fixed in the same solution, and DNA was labeled with YOYO-1. (A) 3-D volume of the largest chromosome of CHO cells reconstructed from serial confocal sections; scale bar, 1 µm. (B) Length of the largest chromosome, diameter of randomly selected chromosomes, and these values expressed as the % of those in 12% PEG; error bars show SEM from measurements of ≥15 chromosomes. (C) Transverse linescans of fluorescence intensity across representative chomosomes labeled with YOYO-1. (D) Representative images of chromosomes incubated in 100 µm K-Hepes buffer with no PEG for 1 h and labeled with YOYO-1. Scale bar, 1 µm.</p>", "links"=>[], "tags"=>["crowding", "chromosome"], "article_id"=>320000, "categories"=>["Physics", "Biochemistry", "Cell Biology", "Genetics", "Biophysics"], "users"=>["Ronald Hancock"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036045.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Influence_of_the_concentration_of_crowding_agent_on_chromosome_dimensions_/320000", "title"=>"Influence of the concentration of crowding agent on chromosome dimensions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 06:08:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/649641"], "description"=>"<p>(A) DNA fragments from chromosomes incubated with micrococcal nuclease, separated on a 2% agarose gel; M, length markers. (B) Proteins extracted from chromosomes in 0.2 N H<sub>2</sub>SO<sub>4</sub> and separated in a 4–20% denaturing SDS-PAGE gel; markers (M) were purified histones from calf thymus. (C) Topoisomerase IIα and (D) SMC2 visualised by immunofluorescence (red); DNA was labeled with YOYO-1 (green). Scale bars, 1 µm.</p>", "links"=>[], "tags"=>["nonhistone", "proteins", "chromosomes", "released"], "article_id"=>320138, "categories"=>["Physics", "Biochemistry", "Cell Biology", "Genetics", "Biophysics"], "users"=>["Ronald Hancock"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036045.g004", "stats"=>{"downloads"=>3, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nucleosomal_structure_and_nonhistone_proteins_of_chromosomes_released_in_12_PEG_/320138", "title"=>"Nucleosomal structure and nonhistone proteins of chromosomes released in 12% PEG.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 06:09:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/649212"], "description"=>"<p>Representative fields of chromosomes cytocentrifuged and fixed in the same medium as that used for cell lysis. (A, B, F) phase-contrast images; (C–E) DNA labeled with YOYO-1. Chromosomes were released in (A) 12% PEG (M<sub>r</sub> 8 kD); (B) 25% PEG; (C) 20% PEG; (D) 40% Ficoll (M<sub>r</sub> 70 kD); (E) 12% dextran (M<sub>r</sub> 10.5 kD). (F) Chromosomes isolated by a conventional method <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036045#pone.0036045-Lewis1\" target=\"_blank\">[29]</a> from a sample of the mitotic cells used in panel A. Magnification is the same in all panels; scale bar in A, 5 µm.</p>", "links"=>[], "tags"=>["metaphase", "chromosomes", "released", "mitotic", "cho", "cells", "containing", "crowding", "macromolecule", "100", "k-hepes"], "article_id"=>319690, "categories"=>["Physics", "Biochemistry", "Cell Biology", "Genetics", "Biophysics"], "users"=>["Ronald Hancock"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036045.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_8211_E_Metaphase_chromosomes_released_from_mitotic_CHO_cells_in_a_solution_containing_a_crowding_macromolecule_in_100_181_M_K_Hepes_buffer_/319690", "title"=>"(A–E) Metaphase chromosomes released from mitotic CHO cells in a solution containing a crowding macromolecule in 100 µM K-Hepes buffer.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 06:07:16"}

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  • {"unique-ip"=>"100", "full-text"=>"112", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"83", "full-text"=>"102", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"119", "full-text"=>"139", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"136", "full-text"=>"158", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"125", "full-text"=>"149", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}

Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[322, 550, 671, 773, 864, 955, 1048, 1135, 1223, 1308, 1387, 1465, 1534, 1602, 1673, 1744, 1813, 1885, 1955, 2026, 2093, 2160, 2228, 2290, 2349]}, {"subject_area"=>"/Biology and life sciences/Cell biology", "average_usage"=>[319, 556, 679, 785, 881, 970, 1062, 1149, 1236, 1323, 1402, 1474, 1545, 1617, 1681, 1754, 1822, 1892, 1963, 2031, 2099, 2165, 2233, 2299, 2359]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[333, 576, 707, 814, 908, 1004, 1104, 1197, 1280, 1370, 1449, 1531, 1603, 1673, 1742, 1817, 1886, 1954, 2025, 2098, 2171, 2234, 2304, 2365, 2431]}, {"subject_area"=>"/Physical sciences", "average_usage"=>[304, 506, 616, 712, 799, 879, 968, 1052, 1134, 1212, 1284, 1357, 1427, 1494, 1557, 1621, 1689, 1756, 1823, 1883, 1944, 1997, 2056, 2118, 2171]}, {"subject_area"=>"/Physical sciences/Chemistry", "average_usage"=>[302, 508, 622, 720, 804, 888, 973, 1054, 1141, 1219, 1299, 1370, 1442, 1511, 1574, 1644, 1711, 1782, 1846, 1911, 1971, 2030, 2097, 2155, 2217]}]}
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