Unique Profile of Ordered Arrangements of Repetitive Elements in the C57BL/6J Mouse Genome Implicating Their Functional Roles
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{"title"=>"Unique profile of ordered arrangements of repetitive elements in the C57BL/6J mouse genome implicating their functional roles", "type"=>"journal", "authors"=>[{"first_name"=>"Young Kwan", "last_name"=>"Lee", "scopus_author_id"=>"27171275200"}, {"first_name"=>"Kang Hoon", "last_name"=>"Lee", "scopus_author_id"=>"55541369900"}, {"first_name"=>"Seon Gyu", "last_name"=>"Kim", "scopus_author_id"=>"55193349400"}, {"first_name"=>"Ramzi", "last_name"=>"Melhem", "scopus_author_id"=>"46062203200"}, {"first_name"=>"Chang Suk", "last_name"=>"Moon", "scopus_author_id"=>"55193123100"}, {"first_name"=>"Sicong", "last_name"=>"Liu", "scopus_author_id"=>"55193681400"}, {"first_name"=>"David G.", "last_name"=>"Greenhalgh", "scopus_author_id"=>"35408382700"}, {"first_name"=>"Kiho", "last_name"=>"Cho", "scopus_author_id"=>"55541792200"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84859957287", "pui"=>"364660935", "pmid"=>"22529984", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0035156", "sgr"=>"84859957287"}, "id"=>"20604c18-04e7-3379-ba9c-703c33648d75", "abstract"=>"The entirety of all protein coding sequences is reported to represent a small fraction (~2%) of the mouse and human genomes; the vast majority of the rest of the genome is presumed to be repetitive elements (REs). In this study, the C57BL/6J mouse reference genome was subjected to an unbiased RE mining to establish a whole-genome profile of RE occurrence and arrangement. The C57BL/6J mouse genome was fragmented into an initial set of 5,321 units of 0.5 Mb, and surveyed for REs using unbiased self-alignment and dot-matrix protocols. The survey revealed that individual chromosomes had unique profiles of RE arrangement structures, named RE arrays. The RE populations in certain genomic regions were arranged into various forms of complexly organized structures using combinations of direct and/or inverse repeats. Some of these RE arrays spanned stretches of over 2 Mb, which may contribute to the structural configuration of the respective genomic regions. There were substantial differences in RE density among the 21 chromosomes, with chromosome Y being the most densely populated. In addition, the RE array population in the mouse chromosomes X and Y was substantially different from those of the reference human chromosomes. Conversion of the dot-matrix data pertaining to a tandem 13-repeat structure within the Ch7.032 genome unit into a line map of known REs revealed a repeat unit of ~11.3 Kb as a mosaic of six different RE types. The data obtained from this study allowed for a comprehensive RE profiling, including the establishment of a library of RE arrays, of the reference mouse genome. Some of these RE arrays may participate in a spectrum of normal and disease biology that are specific for mice.", "link"=>"http://www.mendeley.com/research/unique-profile-ordered-arrangements-repetitive-elements-c57bl6j-mouse-genome-implicating-functional", "reader_count"=>1, "reader_count_by_academic_status"=>{"Student > Ph. D. Student"=>1}, "reader_count_by_user_role"=>{"Student > Ph. D. Student"=>1}, "reader_count_by_subject_area"=>{"Neuroscience"=>1}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/652616"], "description"=>"<p>The 3′-end of the immunoglobulin heavy chain (IGh) is presented as a dot-matrix plot with markings for the various switch regions (in blue). The zoomed-in tandem RE array dot-matrix plot represents the IgM switch region (Sμ). The illustration, involving Sμ and c-<i>Myc</i> gene sequences, depicts the putative translocation event between two sections of the IgM switch region on chromosome 12 and a 40-nucleotide stretch within the c-<i>Myc</i> gene on chromosome 15. One unique stretch of 40 nucleotides in the c-<i>Myc</i> sequence, corresponding to a reported translocation breakpoint in the c-<i>Myc</i> gene, had a high homology (80% identity: 5 mismatches and 2 gaps) with two sections of the IgM switch region tandem array. Ch (mouse chromosome), ex (exon), red triangles (putative translocation breakpoints).</p>", "links"=>[], "tags"=>["tandem", "igm"], "article_id"=>323102, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Young-Kwan Lee", "Kang-Hoon Lee", "Seon-Gyu Kim", "Ramzi Melhem", "Chang-Suk Moon", "Sicong Liu", "David G. Greenhalgh", "Kiho Cho"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035156.g007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Translocation_between_the_tandem_RE_array_of_the_IgM_switch_region_and_the_c_Myc_gene_/323102", "title"=>"Translocation between the tandem RE array of the IgM switch region and the c-<i>Myc</i> gene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:51:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/652467"], "description"=>"<p>The RE arrays identified in the chromosomes X and Y of the reference mouse genome were compared to those from the reference human genome. Four RE arrays unique for the mouse and human chromosomes were selected. Also, four similar RE arrays were identified from the mouse and human chromosomes.</p>", "links"=>[], "tags"=>["arrays", "chromosomes"], "article_id"=>322956, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Young-Kwan Lee", "Kang-Hoon Lee", "Seon-Gyu Kim", "Ramzi Melhem", "Chang-Suk Moon", "Sicong Liu", "David G. Greenhalgh", "Kiho Cho"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035156.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Unique_and_similar_RE_arrays_in_chromosomes_X_and_Y_mouse_vs_human_/322956", "title"=>"Unique and similar RE arrays in chromosomes X and Y: mouse vs. human.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:49:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/651759"], "description"=>"<p>The RE arrays plotted from the genome units/subunits of chromosomes 7, X, and Y are assembled in order of 5′ to 3′. The same data sets are presented in a smaller scale in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035156#pone-0035156-g002\" target=\"_blank\">Fig. 2</a>. The same labeling and identification schedules as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035156#pone-0035156-g002\" target=\"_blank\">Fig. 2</a> are used. A set of subunits derived from one genome unit are grouped with a rectangle.</p>", "links"=>[], "tags"=>["arrays", "chromosomes"], "article_id"=>322248, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Young-Kwan Lee", "Kang-Hoon Lee", "Seon-Gyu Kim", "Ramzi Melhem", "Chang-Suk Moon", "Sicong Liu", "David G. Greenhalgh", "Kiho Cho"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035156.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RE_arrays_of_chromosomes_7_X_and_Y_/322248", "title"=>"RE arrays of chromosomes 7, X, and Y.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:37:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/652211"], "description"=>"<p>A total of 135 unique RE arrays are selected throughout the mouse genome and compiled by chromosome order (1∼19, X, and Y). <b>A</b>. Compilation of RE arrays from a single genome unit or a set of subunits from one genome unit. A set of subunits derived from one genome unit is indicated by a rectangle. The Ch7.032 genome unit is highlighted by a dotted square. <b>B</b>. Compilation of RE arrays spanning consecutive genome units.</p>", "links"=>[], "tags"=>["arrays"], "article_id"=>322705, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Young-Kwan Lee", "Kang-Hoon Lee", "Seon-Gyu Kim", "Ramzi Melhem", "Chang-Suk Moon", "Sicong Liu", "David G. Greenhalgh", "Kiho Cho"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035156.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Compilation_of_unique_RE_arrays_selected_throughout_the_entire_genome_/322705", "title"=>"Compilation of unique RE arrays selected throughout the entire genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:45:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/651457"], "description"=>"<p>The diagram illustrates how a series of sequential half-size subunits are generated from a genome unit of 0.5 Mb, using the Ch7.134 as an example. During each fragmentation event, the 5′-half is designated as “L\" and the 3′-half is designated as “R\", and lowercase and uppercase letters are alternated for sequential fragmentation events. The chromosomal ideogram is adopted from the NCBI mouse genome database. *identification of genome unit, **chromosomal location, Ch (chromosome).</p>", "links"=>[], "tags"=>["fragmentation", "genome", "sequential", "half-size"], "article_id"=>321935, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Young-Kwan Lee", "Kang-Hoon Lee", "Seon-Gyu Kim", "Ramzi Melhem", "Chang-Suk Moon", "Sicong Liu", "David G. Greenhalgh", "Kiho Cho"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035156.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schedule_for_fragmentation_of_a_genome_unit_into_sequential_half_size_subunits_/321935", "title"=>"Schedule for fragmentation of a genome unit into sequential half-size subunits.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:32:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/652768"], "description"=>"<p><b>A</b>. The dot-matrix plot is derived from an unbiased self-alignment of the Ch7.032 genome unit. The REs in the area highlighted with a dotted red line are subjected to a line mapping experiment. <b>B</b>. The RE profile within the tandem 13 repeats of the ∼11.3 Kb unit in the highlighted structure are plotted on a scaled line map using color coding to identify RE types. In addition, <i>Obox4</i> gene sequences are marked within each repeat unit. <b>C</b>. The RE profile of the entire Ch7.032 genome unit of 0.5 Mb are plotted on a scaled line map for all RE types with color coding identification. The dotted rectangle represents the location of the first ∼11.3 Kb repeat unit within the Ch7.032 genome unit. High-resolution line maps (for maps on panels B and C) are accessible through <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035156#pone.0035156.s022\" target=\"_blank\">Figs. S22</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035156#pone.0035156.s023\" target=\"_blank\">S23</a>.</p>", "links"=>[], "tags"=>["genome"], "article_id"=>323260, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Young-Kwan Lee", "Kang-Hoon Lee", "Seon-Gyu Kim", "Ramzi Melhem", "Chang-Suk Moon", "Sicong Liu", "David G. Greenhalgh", "Kiho Cho"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035156.g008", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Line_mapping_of_REs_genes_within_the_Ch7_032_genome_unit_/323260", "title"=>"Line mapping of REs/genes within the Ch7.032 genome unit.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:54:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/651553"], "description"=>"<p>The dot-matrix plots of the self-alignment data derived from a total of 5,321 genome units of 0.5 Mb, in addition to 41 subunits of varying sizes, which cover the entire mouse genome, are compiled by chromosome order (1∼19, X, and Y). Each genome unit/subunit is represented by a square and unit identifications are indicated only for the ones on the far left of each row. Genome units without any sequence information (gap) are indicated with a white square. Grey rectangles indicate partial gaps. Ideograms for individual chromosomes, which are adopted from the NCBI mouse genome database, are included as a reference. A set of subunits derived from one genome unit are grouped with a rectangle. A detailed plot view of the RE occurrence and arrangement structure is available through the electronic supplementary figures.</p>", "links"=>[], "tags"=>["occurrence"], "article_id"=>322041, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Young-Kwan Lee", "Kang-Hoon Lee", "Seon-Gyu Kim", "Ramzi Melhem", "Chang-Suk Moon", "Sicong Liu", "David G. Greenhalgh", "Kiho Cho"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035156.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Whole_genome_view_of_occurrence_and_arrangement_structure_of_REs_/322041", "title"=>"Whole-genome view of occurrence and arrangement structure of REs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:34:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/337518", "https://ndownloader.figshare.com/files/337645", "https://ndownloader.figshare.com/files/337781", "https://ndownloader.figshare.com/files/337871", "https://ndownloader.figshare.com/files/337960", "https://ndownloader.figshare.com/files/338082", "https://ndownloader.figshare.com/files/338164", "https://ndownloader.figshare.com/files/338239", "https://ndownloader.figshare.com/files/338311", "https://ndownloader.figshare.com/files/338387", "https://ndownloader.figshare.com/files/338491", "https://ndownloader.figshare.com/files/338555", "https://ndownloader.figshare.com/files/338612", "https://ndownloader.figshare.com/files/338686", "https://ndownloader.figshare.com/files/338839", "https://ndownloader.figshare.com/files/338932", "https://ndownloader.figshare.com/files/339010", "https://ndownloader.figshare.com/files/339105", "https://ndownloader.figshare.com/files/339176", "https://ndownloader.figshare.com/files/339249", "https://ndownloader.figshare.com/files/339359", "https://ndownloader.figshare.com/files/339424", "https://ndownloader.figshare.com/files/339601"], "description"=>"<div><p>The entirety of all protein coding sequences is reported to represent a small fraction (∼2%) of the mouse and human genomes; the vast majority of the rest of the genome is presumed to be repetitive elements (REs). In this study, the C57BL/6J mouse reference genome was subjected to an unbiased RE mining to establish a whole-genome profile of RE occurrence and arrangement. The C57BL/6J mouse genome was fragmented into an initial set of 5,321 units of 0.5 Mb, and surveyed for REs using unbiased self-alignment and dot-matrix protocols. The survey revealed that individual chromosomes had unique profiles of RE arrangement structures, named RE arrays. The RE populations in certain genomic regions were arranged into various forms of complexly organized structures using combinations of direct and/or inverse repeats. Some of these RE arrays spanned stretches of over 2 Mb, which may contribute to the structural configuration of the respective genomic regions. There were substantial differences in RE density among the 21 chromosomes, with chromosome Y being the most densely populated. In addition, the RE array population in the mouse chromosomes X and Y was substantially different from those of the reference human chromosomes. Conversion of the dot-matrix data pertaining to a tandem 13-repeat structure within the Ch7.032 genome unit into a line map of known REs revealed a repeat unit of ∼11.3 Kb as a mosaic of six different RE types. The data obtained from this study allowed for a comprehensive RE profiling, including the establishment of a library of RE arrays, of the reference mouse genome. Some of these RE arrays may participate in a spectrum of normal and disease biology that are specific for mice.</p> </div>", "links"=>[], "tags"=>["ordered", "arrangements", "repetitive", "elements", "genome", "implicating", "roles"], "article_id"=>126712, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Young-Kwan Lee", "Kang-Hoon Lee", "Seon-Gyu Kim", "Ramzi Melhem", "Chang-Suk Moon", "Sicong Liu", "David G. Greenhalgh", "Kiho Cho"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0035156.s001", "https://dx.doi.org/10.1371/journal.pone.0035156.s002", "https://dx.doi.org/10.1371/journal.pone.0035156.s003", "https://dx.doi.org/10.1371/journal.pone.0035156.s004", "https://dx.doi.org/10.1371/journal.pone.0035156.s005", "https://dx.doi.org/10.1371/journal.pone.0035156.s006", "https://dx.doi.org/10.1371/journal.pone.0035156.s007", "https://dx.doi.org/10.1371/journal.pone.0035156.s008", "https://dx.doi.org/10.1371/journal.pone.0035156.s009", "https://dx.doi.org/10.1371/journal.pone.0035156.s010", "https://dx.doi.org/10.1371/journal.pone.0035156.s011", "https://dx.doi.org/10.1371/journal.pone.0035156.s012", "https://dx.doi.org/10.1371/journal.pone.0035156.s013", "https://dx.doi.org/10.1371/journal.pone.0035156.s014", "https://dx.doi.org/10.1371/journal.pone.0035156.s015", "https://dx.doi.org/10.1371/journal.pone.0035156.s016", "https://dx.doi.org/10.1371/journal.pone.0035156.s017", "https://dx.doi.org/10.1371/journal.pone.0035156.s018", "https://dx.doi.org/10.1371/journal.pone.0035156.s019", "https://dx.doi.org/10.1371/journal.pone.0035156.s020", "https://dx.doi.org/10.1371/journal.pone.0035156.s021", "https://dx.doi.org/10.1371/journal.pone.0035156.s022", "https://dx.doi.org/10.1371/journal.pone.0035156.s023"], "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Unique_Profile_of_Ordered_Arrangements_of_Repetitive_Elements_in_the_C57BL_6J_Mouse_Genome_Implicating_Their_Functional_Roles/126712", "title"=>"Unique Profile of Ordered Arrangements of Repetitive Elements in the C57BL/6J Mouse Genome Implicating Their Functional Roles", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-04-18 01:51:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/651965"], "description"=>"<p><b>A</b>. RE density (inverse RGB value) of individual chromosomes. The average RE density of individual genome units/subunits, which are collected as an inverse RGB value, are plotted (plus strand: 5′ to 3′ direction) for each chromosome. Gap regions within each chromosome are indicated with an arrow (≤3 Mb) or arrow with bracket (>3 Mb). <b>B</b>. Average RE density of each chromosome. There are significant differences in the profile of RE density among the 21 chromosomes. *chromosome with the highest overall RE density, **chromosome with the highest overall RE density within the limited sequence information available.</p>", "links"=>[], "tags"=>["genome"], "article_id"=>322451, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Young-Kwan Lee", "Kang-Hoon Lee", "Seon-Gyu Kim", "Ramzi Melhem", "Chang-Suk Moon", "Sicong Liu", "David G. Greenhalgh", "Kiho Cho"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035156.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_average_RE_density_of_genome_units_subunits_of_individual_chromosomes_/322451", "title"=>"Distribution of average RE density of genome units/subunits of individual chromosomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:40:51"}

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Relative Metric

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