Filling in the Gap of Human Chromosome 4: Single Molecule Real Time Sequencing of Macrosatellite Repeats in the Facioscapulohumeral Muscular Dystrophy Locus
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{"title"=>"Filling in the gap of human chromosome 4: Single molecule real time sequencing of macrosatellite repeats in the facioscapulohumeral muscular dystrophy locus", "type"=>"journal", "authors"=>[{"first_name"=>"Masaki Suimye", "last_name"=>"Morioka", "scopus_author_id"=>"8666308100"}, {"first_name"=>"Miwako", "last_name"=>"Kitazume", "scopus_author_id"=>"57188703671"}, {"first_name"=>"Ken", "last_name"=>"Osaki", "scopus_author_id"=>"57188694924"}, {"first_name"=>"Jonathan", "last_name"=>"Wood", "scopus_author_id"=>"56325214300"}, {"first_name"=>"Yujiro", "last_name"=>"Tanaka", "scopus_author_id"=>"55499612900"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "doi"=>"10.1371/journal.pone.0151963", "sgr"=>"84962374612", "scopus"=>"2-s2.0-84962374612", "isbn"=>"1932-6203 (Electronic)\r1932-6203 (Linking)", "pmid"=>"27002334", "pui"=>"609296175"}, "id"=>"471e8c22-d8df-3456-9f89-52ef7bce4fa9", "abstract"=>"A majority of facioscapulohumeral muscular dystrophy (FSHD) is caused by contraction of macrosatellite repeats called D4Z4 that are located in the subtelomeric region of human chromosome 4q35. Sequencing the FSHD locus has been technically challenging due to its long size and nearly identical nature of repeat elements. Here we report sequencing and partial assembly of a BAC clone carrying an entire FSHD locus by a single molecule real time (SMRT) sequencing technology which could produce long reads up to about 18 kb containing D4Z4 repeats. De novo assembly by Hierarchical Genome Assembly Process 1 (HGAP.1) yielded a contig of 41 kb containing all but a part of the most distal D4Z4 element. The validity of the sequence model was confirmed by an independent approach employing anchored multiple sequence alignment by Kalign using reads containing unique flanking sequences. Our data will provide a basis for further optimization of sequencing and assembly conditions of D4Z4.", "link"=>"http://www.mendeley.com/research/filling-gap-human-chromosome-4-single-molecule-real-time-sequencing-macrosatellite-repeats-facioscap", "reader_count"=>16, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Other"=>1, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Other"=>1, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>9, "Medicine and Dentistry"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"United Kingdom"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/4877818"], "description"=>"<p>Pair-wise comparisons between P4C2-Kalign, P5C3-Kalign, and P4C2-HGAP.1 were carried out by CLC Main Workbench (version 6). Percent identities and number of nucleotide differences are shown.</p>", "links"=>[], "tags"=>["Facioscapulohumeral Muscular Dystrophy Locus", "sequence", "D 4Z", "sequencing", "BAC", "assembly", "D 4Z element", "chromosome 4 q 35. Sequencing", "HGAP", "Hierarchical Genome Assembly Process 1", "kb", "FSHD locus", "SMRT"], "article_id"=>3136609, "categories"=>["Biophysics", "Physical Sciences not elsewhere classified", "Genetics", "Molecular Biology", "Neuroscience", "Biotechnology", "Evolutionary Biology", "Chemical Sciences not elsewhere classified", "Immunology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Virology"], "users"=>["Masaki Suimye Morioka", "Miwako Kitazume", "Ken Osaki", "Jonathan Wood", "Yujiro Tanaka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0151963.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Pair_wise_comparisons_of_D4Z4_sequences_obtained_by_independent_methods_/3136609", "title"=>"Pair-wise comparisons of D4Z4 sequences obtained by independent methods.", "pos_in_sequence"=>10, "defined_type"=>3, "published_date"=>"2016-03-22 06:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/4877689"], "description"=>"<p>To avoid misalignment of repetitive elements, quality-filtered subreads containing D4Z4 and flanking unique sequences were first selected and trimmed by either 5' or 3' unique region. Sequences at the 3' end were reverse complemented to bring unique sequences to the 5' end. After generating multiple sequence alignment by Kalign, consensus sequences were generated by calling bases above thresholds (13% for P4C2, 14% for P5C3).</p>", "links"=>[], "tags"=>["Facioscapulohumeral Muscular Dystrophy Locus", "sequence", "D 4Z", "sequencing", "BAC", "assembly", "D 4Z element", "chromosome 4 q 35. Sequencing", "HGAP", "Hierarchical Genome Assembly Process 1", "kb", "FSHD locus", "SMRT"], "article_id"=>3136516, "categories"=>["Biophysics", "Physical Sciences not elsewhere classified", "Genetics", "Molecular Biology", "Neuroscience", "Biotechnology", "Evolutionary Biology", "Chemical Sciences not elsewhere classified", "Immunology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Virology"], "users"=>["Masaki Suimye Morioka", "Miwako Kitazume", "Ken Osaki", "Jonathan Wood", "Yujiro Tanaka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0151963.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Scheme_of_anchored_multiple_sequence_alignment_/3136516", "title"=>"Scheme of anchored multiple sequence alignment.", "pos_in_sequence"=>5, "defined_type"=>1, "published_date"=>"2016-03-22 06:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/4877662"], "description"=>"<p>A. GC contents of D4Z4 repeats and the rest of the BAC clone RP11-242C23 (P4C2 chemistry). Red lines indicate GC counts per read and blue lines indicate theoretically modeled normal distributions. D4Z4 repeats are highly rich in GC. B. Box plots showing the predicted per-base quality scores of sequenced reads at various positions from 5' to 3' ends for D4Z4 repeats and the rest.</p>", "links"=>[], "tags"=>["Facioscapulohumeral Muscular Dystrophy Locus", "sequence", "D 4Z", "sequencing", "BAC", "assembly", "D 4Z element", "chromosome 4 q 35. Sequencing", "HGAP", "Hierarchical Genome Assembly Process 1", "kb", "FSHD locus", "SMRT"], "article_id"=>3136486, "categories"=>["Biophysics", "Physical Sciences not elsewhere classified", "Genetics", "Molecular Biology", "Neuroscience", "Biotechnology", "Evolutionary Biology", "Chemical Sciences not elsewhere classified", "Immunology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Virology"], "users"=>["Masaki Suimye Morioka", "Miwako Kitazume", "Ken Osaki", "Jonathan Wood", "Yujiro Tanaka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0151963.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/GC_contents_and_read_qualities_of_D4Z4_repeat_region_and_the_rest_/3136486", "title"=>"GC contents and read qualities of D4Z4 repeat region and the rest.", "pos_in_sequence"=>3, "defined_type"=>1, "published_date"=>"2016-03-22 06:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/4877554", "https://ndownloader.figshare.com/files/4877608", "https://ndownloader.figshare.com/files/4877599", "https://ndownloader.figshare.com/files/4877596", "https://ndownloader.figshare.com/files/4877590", "https://ndownloader.figshare.com/files/4877587", "https://ndownloader.figshare.com/files/4877578", "https://ndownloader.figshare.com/files/4877569", "https://ndownloader.figshare.com/files/4877557", "https://ndownloader.figshare.com/files/4877617"], "description"=>"<div><p>A majority of facioscapulohumeral muscular dystrophy (FSHD) is caused by contraction of macrosatellite repeats called D4Z4 that are located in the subtelomeric region of human chromosome 4q35. Sequencing the FSHD locus has been technically challenging due to its long size and nearly identical nature of repeat elements. Here we report sequencing and partial assembly of a BAC clone carrying an entire FSHD locus by a single molecule real time (SMRT) sequencing technology which could produce long reads up to about 18 kb containing D4Z4 repeats. De novo assembly by Hierarchical Genome Assembly Process 1 (HGAP.1) yielded a contig of 41 kb containing all but a part of the most distal D4Z4 element. The validity of the sequence model was confirmed by an independent approach employing anchored multiple sequence alignment by Kalign using reads containing unique flanking sequences. Our data will provide a basis for further optimization of sequencing and assembly conditions of D4Z4.</p></div>", "links"=>[], "tags"=>["Facioscapulohumeral Muscular Dystrophy Locus", "sequence", "D 4Z", "sequencing", "BAC", "assembly", "D 4Z element", "chromosome 4 q 35. Sequencing", "HGAP", "Hierarchical Genome Assembly Process 1", "kb", "FSHD locus", "SMRT"], "article_id"=>3136426, "categories"=>["Biophysics", "Physical Sciences not elsewhere classified", "Genetics", "Molecular Biology", "Neuroscience", "Biotechnology", "Evolutionary Biology", "Chemical Sciences not elsewhere classified", "Immunology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Virology"], "users"=>["Masaki Suimye Morioka", "Miwako Kitazume", "Ken Osaki", "Jonathan Wood", "Yujiro Tanaka"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0151963.s001", "https://dx.doi.org/10.1371/journal.pone.0151963.s009", "https://dx.doi.org/10.1371/journal.pone.0151963.s008", "https://dx.doi.org/10.1371/journal.pone.0151963.s007", "https://dx.doi.org/10.1371/journal.pone.0151963.s006", "https://dx.doi.org/10.1371/journal.pone.0151963.s005", "https://dx.doi.org/10.1371/journal.pone.0151963.s004", "https://dx.doi.org/10.1371/journal.pone.0151963.s003", "https://dx.doi.org/10.1371/journal.pone.0151963.s002", "https://dx.doi.org/10.1371/journal.pone.0151963.s010"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Filling_in_the_Gap_of_Human_Chromosome_4_Single_Molecule_Real_Time_Sequencing_of_Macrosatellite_Repeats_in_the_Facioscapulohumeral_Muscular_Dystrophy_Locus/3136426", "title"=>"Filling in the Gap of Human Chromosome 4: Single Molecule Real Time Sequencing of Macrosatellite Repeats in the Facioscapulohumeral Muscular Dystrophy Locus", "pos_in_sequence"=>1, "defined_type"=>4, "published_date"=>"2016-03-22 06:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/4877731"], "description"=>"<p>Statistics of filtered subreads of the two BAC clones. Numbers of filtered subreads and quality scores are similar for three samples.</p>", "links"=>[], "tags"=>["Facioscapulohumeral Muscular Dystrophy Locus", "sequence", "D 4Z", "sequencing", "BAC", "assembly", "D 4Z element", "chromosome 4 q 35. Sequencing", "HGAP", "Hierarchical Genome Assembly Process 1", "kb", "FSHD locus", "SMRT"], "article_id"=>3136555, "categories"=>["Biophysics", "Physical Sciences not elsewhere classified", "Genetics", "Molecular Biology", "Neuroscience", "Biotechnology", "Evolutionary Biology", "Chemical Sciences not elsewhere classified", "Immunology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Virology"], "users"=>["Masaki Suimye Morioka", "Miwako Kitazume", "Ken Osaki", "Jonathan Wood", "Yujiro Tanaka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0151963.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Statistics_of_filtered_subreads_/3136555", "title"=>"Statistics of filtered subreads.", "pos_in_sequence"=>7, "defined_type"=>3, "published_date"=>"2016-03-22 06:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/4877791"], "description"=>"<p>Filtered subreads of P4C2 and P5C3 data were selected and trimmed by 5' or 3' flanking sequences. Those containing the unique NDE or pLAM elements were subjected to multiple sequence alignment by Kalign. The longest subread of P5C3 corresponds to about 5.5 copies of D4Z4.</p>", "links"=>[], "tags"=>["Facioscapulohumeral Muscular Dystrophy Locus", "sequence", "D 4Z", "sequencing", "BAC", "assembly", "D 4Z element", "chromosome 4 q 35. Sequencing", "HGAP", "Hierarchical Genome Assembly Process 1", "kb", "FSHD locus", "SMRT"], "article_id"=>3136588, "categories"=>["Biophysics", "Physical Sciences not elsewhere classified", "Genetics", "Molecular Biology", "Neuroscience", "Biotechnology", "Evolutionary Biology", "Chemical Sciences not elsewhere classified", "Immunology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Virology"], "users"=>["Masaki Suimye Morioka", "Miwako Kitazume", "Ken Osaki", "Jonathan Wood", "Yujiro Tanaka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0151963.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Statistics_of_anchored_subreads_/3136588", "title"=>"Statistics of anchored subreads.", "pos_in_sequence"=>9, "defined_type"=>3, "published_date"=>"2016-03-22 06:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/4877698"], "description"=>"<p>A total of D4Z4 sequences obtained by either anchored multiple sequence alignment (P5C3_ and P4C2_ followed by positions in the array) or resequencing using longest P5C3 subreads containing D4Z4 and 5' or 3' flanking unique sequences (HGAP_ followed by positions in the array) were aligned to each other to assess sequence variations. Depicted are regions upstream of ATG translation start site that contain known motifs such as PRE, YY1, GC box, and TACAA box.</p>", "links"=>[], "tags"=>["Facioscapulohumeral Muscular Dystrophy Locus", "sequence", "D 4Z", "sequencing", "BAC", "assembly", "D 4Z element", "chromosome 4 q 35. Sequencing", "HGAP", "Hierarchical Genome Assembly Process 1", "kb", "FSHD locus", "SMRT"], "article_id"=>3136528, "categories"=>["Biophysics", "Physical Sciences not elsewhere classified", "Genetics", "Molecular Biology", "Neuroscience", "Biotechnology", "Evolutionary Biology", "Chemical Sciences not elsewhere classified", "Immunology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Virology"], "users"=>["Masaki Suimye Morioka", "Miwako Kitazume", "Ken Osaki", "Jonathan Wood", "Yujiro Tanaka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0151963.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Conservation_of_transcription_factor_binding_motifs_in_the_D4Z4_array_/3136528", "title"=>"Conservation of transcription factor binding motifs in the D4Z4 array.", "pos_in_sequence"=>6, "defined_type"=>1, "published_date"=>"2016-03-22 06:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/4877641"], "description"=>"<p>A. Organization of the FSHD locus of the human chromosome 4 subtelomeric region. The D4Z4 repeat unit is represented by trapezoid with an inner shaded rectangle of the DUX4 coding region. The copy number of D4Z4 that causes the disease depends on the genetic background of secondary modifiers such as SMCHD1. B. Alignments of polished contigs of CH16-291A23 (P4C2), RP11-242C23 (P4C2), and RP11-242C23 (P5C3) to a reference, i.e. Genebank accession number CT476828 that comprises 13 copies of an identical D4Z4 unit. Contig names are indicated above grey boxes, where black dots represent gaps. White boxes are contigs of low quality scores. For CH16-291A23 (P4C2) and RP11-242C23 (P5C3), contigs containing D4Z4 units are mapped multiple times to the D4Z4 repeat region since they cannot be uniquely mapped. Note that scf180000000014 has not been correctly assembled and consists of two fragments, one of which contains an inverted D4Z4 unit (DUX4c).</p>", "links"=>[], "tags"=>["Facioscapulohumeral Muscular Dystrophy Locus", "sequence", "D 4Z", "sequencing", "BAC", "assembly", "D 4Z element", "chromosome 4 q 35. Sequencing", "HGAP", "Hierarchical Genome Assembly Process 1", "kb", "FSHD locus", "SMRT"], "article_id"=>3136468, "categories"=>["Biophysics", "Physical Sciences not elsewhere classified", "Genetics", "Molecular Biology", "Neuroscience", "Biotechnology", "Evolutionary Biology", "Chemical Sciences not elsewhere classified", "Immunology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Virology"], "users"=>["Masaki Suimye Morioka", "Miwako Kitazume", "Ken Osaki", "Jonathan Wood", "Yujiro Tanaka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0151963.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Elements_of_the_FSHD_locus_and_positions_of_polished_contigs_of_BAC_clones_/3136468", "title"=>"Elements of the FSHD locus and positions of polished contigs of BAC clones.", "pos_in_sequence"=>2, "defined_type"=>1, "published_date"=>"2016-03-22 06:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/4877674"], "description"=>"<p>A-E. Horizontal axis is the positon in each contig and the vertical axis is the coverage for the five contigs generated by HGAP.1 analysis of RP11-242C23 (P4C2). Contigs that can be mapped to a reference, i.e. Genebank accession number CT476828, are illustrated in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151963#pone.0151963.g001\" target=\"_blank\">Fig 1B</a>. Sharp drops correspond to EcoRV sites. The contig containing D4Z4 repeats (C) shows highly skewed coverage distribution, suggesting misalignment in the middle region. F. Frequencies of different levels (depth) of coverage are shown.</p>", "links"=>[], "tags"=>["Facioscapulohumeral Muscular Dystrophy Locus", "sequence", "D 4Z", "sequencing", "BAC", "assembly", "D 4Z element", "chromosome 4 q 35. Sequencing", "HGAP", "Hierarchical Genome Assembly Process 1", "kb", "FSHD locus", "SMRT"], "article_id"=>3136501, "categories"=>["Biophysics", "Physical Sciences not elsewhere classified", "Genetics", "Molecular Biology", "Neuroscience", "Biotechnology", "Evolutionary Biology", "Chemical Sciences not elsewhere classified", "Immunology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Virology"], "users"=>["Masaki Suimye Morioka", "Miwako Kitazume", "Ken Osaki", "Jonathan Wood", "Yujiro Tanaka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0151963.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Coverage_of_RP11_242C23_sequencing_by_P4C2_chemistry_/3136501", "title"=>"Coverage of RP11-242C23 sequencing by P4C2 chemistry.", "pos_in_sequence"=>4, "defined_type"=>1, "published_date"=>"2016-03-22 06:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/4877776"], "description"=>"<p>Basic statistics of contigs generated from two BAC clones and two kinds of library construction chemistries. CH16-291A23 and RP11-242C23 with P4C2 chemistry generated contigs containing D4Z4 repeats. RP11-242C23 prepared by P5C3 chemistry failed to produce contigs with D4Z4 repeats.</p>", "links"=>[], "tags"=>["Facioscapulohumeral Muscular Dystrophy Locus", "sequence", "D 4Z", "sequencing", "BAC", "assembly", "D 4Z element", "chromosome 4 q 35. Sequencing", "HGAP", "Hierarchical Genome Assembly Process 1", "kb", "FSHD locus", "SMRT"], "article_id"=>3136573, "categories"=>["Biophysics", "Physical Sciences not elsewhere classified", "Genetics", "Molecular Biology", "Neuroscience", "Biotechnology", "Evolutionary Biology", "Chemical Sciences not elsewhere classified", "Immunology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Virology"], "users"=>["Masaki Suimye Morioka", "Miwako Kitazume", "Ken Osaki", "Jonathan Wood", "Yujiro Tanaka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0151963.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Statistics_of_contigs_/3136573", "title"=>"Statistics of contigs.", "pos_in_sequence"=>8, "defined_type"=>3, "published_date"=>"2016-03-22 06:26:53"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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