Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
Publication Date
December 01, 2011
Journal
PLOS Genetics
Authors
A. P. Jason De Koning, Wanjun Gu, Todd A. Castoe, Mark A. Batzer, et al
Volume
7
Issue
12
Pages
e1002384
DOI
https://dx.plos.org/10.1371/journal.pgen.1002384
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1002384
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22144907
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228813
Europe PMC
http://europepmc.org/abstract/MED/22144907
Web of Science
000299167900005
Scopus
84855281420
Mendeley
http://www.mendeley.com/research/repetitive-elements-comprise-twothirds-human-genome
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CiteULike | Further Information

Mendeley | Further Information

{"title"=>"Repetitive elements may comprise over Two-Thirds of the human genome", "type"=>"journal", "authors"=>[{"first_name"=>"A. P Jason", "last_name"=>"de Koning", "scopus_author_id"=>"7005690019"}, {"first_name"=>"Wanjun", "last_name"=>"Gu", "scopus_author_id"=>"7202449029"}, {"first_name"=>"Todd A.", "last_name"=>"Castoe", "scopus_author_id"=>"6602980445"}, {"first_name"=>"Mark A.", "last_name"=>"Batzer", "scopus_author_id"=>"7006870341"}, {"first_name"=>"David D.", "last_name"=>"Pollock", "scopus_author_id"=>"7202569082"}], "year"=>2011, "source"=>"PLoS Genetics", "identifiers"=>{"pui"=>"364024489", "sgr"=>"84855281420", "pmid"=>"22144907", "scopus"=>"2-s2.0-84855281420", "isbn"=>"22144907", "doi"=>"10.1371/journal.pgen.1002384", "issn"=>"15537390"}, "id"=>"80053548-1d26-3f1a-9bd7-b6cbad6afb17", "abstract"=>"Transposable elements (TEs) are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. Using this approach, about half of the human genome has been previously identified as TEs and low-complexity repeats. We recently developed a highly sensitive alternative de novo strategy, P-clouds, that instead searches for clusters of high-abundance oligonucleotides that are related in sequence space (oligo \"clouds\"). We show here that P-clouds predicts >840 Mbp of additional repetitive sequences in the human genome, thus suggesting that 66%-69% of the human genome is repetitive or repeat-derived. To investigate this remarkable difference, we conducted detailed analyses of the ability of both P-clouds and a commonly used conventional approach, RepeatMasker (RM), to detect different sized fragments of the highly abundant human Alu and MIR SINEs. RM can have surprisingly low sensitivity for even moderately long fragments, in contrast to P-clouds, which has good sensitivity down to small fragment sizes (∼25 bp). Although short fragments have a high intrinsic probability of being false positives, we performed a probabilistic annotation that reflects this fact. We further developed \"element-specific\" P-clouds (ESPs) to identify novel Alu and MIR SINE elements, and using it we identified ∼100 Mb of previously unannotated human elements. ESP estimates of new MIR sequences are in good agreement with RM-based predictions of the amount that RM missed. These results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed.", "link"=>"http://www.mendeley.com/research/repetitive-elements-comprise-twothirds-human-genome", "reader_count"=>518, "reader_count_by_academic_status"=>{"Unspecified"=>8, "Professor > Associate Professor"=>23, "Librarian"=>1, "Student > Doctoral Student"=>26, "Researcher"=>130, "Student > Ph. D. 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Student"=>153, "Student > Postgraduate"=>20, "Other"=>12, "Student > Master"=>67, "Student > Bachelor"=>53, "Lecturer"=>4, "Lecturer > Senior Lecturer"=>2, "Professor"=>19}, "reader_count_by_subject_area"=>{"Unspecified"=>21, "Agricultural and Biological Sciences"=>338, "Philosophy"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Chemistry"=>3, "Computer Science"=>20, "Engineering"=>5, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>84, "Nursing and Health Professions"=>2, "Mathematics"=>3, "Medicine and Dentistry"=>28, "Neuroscience"=>2, "Sports and Recreations"=>1, "Physics and Astronomy"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>28}, "Social Sciences"=>{"Social Sciences"=>1}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Mathematics"=>{"Mathematics"=>3}, "Unspecified"=>{"Unspecified"=>21}, "Environmental Science"=>{"Environmental Science"=>4}, "Engineering"=>{"Engineering"=>5}, "Chemistry"=>{"Chemistry"=>3}, "Neuroscience"=>{"Neuroscience"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>338}, "Computer Science"=>{"Computer Science"=>20}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>84}, "Philosophy"=>{"Philosophy"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"United States"=>20, "Egypt"=>1, "United Kingdom"=>8, "Malaysia"=>1, "Portugal"=>1, "Russia"=>2, "Spain"=>5, "Canada"=>1, "Sweden"=>3, "Czech Republic"=>1, "Netherlands"=>1, "Austria"=>1, "Norway"=>1, "Finland"=>1, "Brazil"=>5, "South Africa"=>1, "Italy"=>3, "France"=>7, "Chile"=>1, "Germany"=>8}, "group_count"=>27}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/707818"], "description"=>"<p>Results are displayed as a percentage of the ungapped genome assembly length. A) Consensus results prior to this study indicate that <50% of the genome is repetitive (<i>RepeatMasker</i>). B) Analysis using <i>P-clouds</i> suggests more than two-thirds of the genome is repetitive or repeat-derived.</p>", "links"=>[], "tags"=>["repeatmasker", "annotation"], "article_id"=>378176, "categories"=>["Mathematics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["A. P. Jason de Koning", "Wanjun Gu", "Todd A. Castoe", "Mark A. Batzer", "David D. Pollock"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002384.g002", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_P_clouds_and_RepeatMasker_annotation_of_the_repeat_structure_of_the_human_genome_/378176", "title"=>"<i>P</i>-clouds and RepeatMasker annotation of the repeat structure of the human genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-01 02:16:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/358706", "https://ndownloader.figshare.com/files/358758", "https://ndownloader.figshare.com/files/358808", "https://ndownloader.figshare.com/files/358830", "https://ndownloader.figshare.com/files/358860", "https://ndownloader.figshare.com/files/358878", "https://ndownloader.figshare.com/files/358903", "https://ndownloader.figshare.com/files/358919", "https://ndownloader.figshare.com/files/358976", "https://ndownloader.figshare.com/files/359001", "https://ndownloader.figshare.com/files/359018", "https://ndownloader.figshare.com/files/359037", "https://ndownloader.figshare.com/files/359096"], "description"=>"<div><p>Transposable elements (TEs) are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. Using this approach, about half of the human genome has been previously identified as TEs and low-complexity repeats. We recently developed a highly sensitive alternative <em>de novo</em> strategy, <em>P-clouds</em>, that instead searches for clusters of high-abundance oligonucleotides that are related in sequence space (oligo “clouds”). We show here that <em>P-clouds</em> predicts >840 Mbp of additional repetitive sequences in the human genome, thus suggesting that 66%–69% of the human genome is repetitive or repeat-derived. To investigate this remarkable difference, we conducted detailed analyses of the ability of both <em>P-clouds</em> and a commonly used conventional approach, <em>RepeatMasker</em> (<em>RM</em>), to detect different sized fragments of the highly abundant human Alu and MIR SINEs. RM can have surprisingly low sensitivity for even moderately long fragments, in contrast to <em>P-clouds</em>, which has good sensitivity down to small fragment sizes (∼25 bp). Although short fragments have a high intrinsic probability of being false positives, we performed a probabilistic annotation that reflects this fact. We further developed “element-specific” <em>P-clouds</em> (ESPs) to identify novel Alu and MIR SINE elements, and using it we identified ∼100 Mb of previously unannotated human elements. ESP estimates of new <em>MIR</em> sequences are in good agreement with RM-based predictions of the amount that RM missed. These results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed.</p> </div>", "links"=>[], "tags"=>["repetitive", "elements", "genome"], "article_id"=>130924, "categories"=>["Mathematics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["A. P. Jason de Koning", "Wanjun Gu", "Todd A. Castoe", "Mark A. Batzer", "David D. Pollock"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002384.s001", "https://dx.doi.org/10.1371/journal.pgen.1002384.s002", "https://dx.doi.org/10.1371/journal.pgen.1002384.s003", "https://dx.doi.org/10.1371/journal.pgen.1002384.s004", "https://dx.doi.org/10.1371/journal.pgen.1002384.s005", "https://dx.doi.org/10.1371/journal.pgen.1002384.s006", "https://dx.doi.org/10.1371/journal.pgen.1002384.s007", "https://dx.doi.org/10.1371/journal.pgen.1002384.s008", "https://dx.doi.org/10.1371/journal.pgen.1002384.s009", "https://dx.doi.org/10.1371/journal.pgen.1002384.s010", "https://dx.doi.org/10.1371/journal.pgen.1002384.s011", "https://dx.doi.org/10.1371/journal.pgen.1002384.s012", "https://dx.doi.org/10.1371/journal.pgen.1002384.s013"], "stats"=>{"downloads"=>48, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Repetitive_Elements_May_Comprise_Over_Two_Thirds_of_the_Human_Genome/130924", "title"=>"Repetitive Elements May Comprise Over Two-Thirds of the Human Genome", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-12-01 00:15:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/708112"], "description"=>"<p>A) <i>Alu</i> regions. B) <i>MIR</i> regions. Identification success is displayed as a running average of 10 bp starting positions.</p>", "links"=>[], "tags"=>["detection", "fragments", "full-length"], "article_id"=>378472, "categories"=>["Mathematics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["A. P. Jason de Koning", "Wanjun Gu", "Todd A. Castoe", "Mark A. Batzer", "David D. Pollock"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002384.g005", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percent_detection_success_for_fragments_of_known_full_length_SINE_elements_/378472", "title"=>"Percent detection success for fragments of known full-length <i>SINE</i> elements.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-01 02:21:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/707749"], "description"=>"<p>A) True data distribution representing divergence within a TE family from a master element sequence (center). B) Consensus sequence based search throws away information by collapsing observed data to a single sequence. C) <i>P-clouds</i> clusters related high-abundance oligos, thus providing better coverage of sequence space.</p>", "links"=>[], "tags"=>["genetics and genomics", "molecular biology", "Evolutionary biology", "mathematics"], "article_id"=>378101, "categories"=>["Mathematics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["A. P. Jason de Koning", "Wanjun Gu", "Todd A. Castoe", "Mark A. Batzer", "David D. Pollock"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002384.g001", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principles_of_repeat_identification_using_P_clouds_/378101", "title"=>"Principles of repeat identification using <i>P</i>-clouds.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-01 02:15:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/707953"], "description"=>"<p>A) The percentage of nucleotides and repeats for each family or repeat classification group. B) The number of nucleotides annotated or missed.</p>", "links"=>[], "tags"=>["previously-identified", "transposable", "elements", "annotated"], "article_id"=>378310, "categories"=>["Mathematics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["A. P. Jason de Koning", "Wanjun Gu", "Todd A. Castoe", "Mark A. Batzer", "David D. Pollock"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002384.g003", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percentage_of_previously_identified_transposable_elements_annotated_by_P_clouds_/378310", "title"=>"Percentage of previously-identified transposable elements annotated by <i>P-clouds</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-01 02:18:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/708299"], "description"=>"<p>Total repetitive sequence detected by either RepeatMasker or <i>P-clouds</i> was 2.23 Gbp (out of a total 2.85 Gbp sequence in the ungapped assembly).</p>", "links"=>[], "tags"=>["genome", "repetitive"], "article_id"=>378659, "categories"=>["Mathematics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["A. P. Jason de Koning", "Wanjun Gu", "Todd A. Castoe", "Mark A. Batzer", "David D. Pollock"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002384.t001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overlap_between_genome_features_and_repetitive_regions_/378659", "title"=>"Overlap between genome features and repetitive regions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-12-01 02:24:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/708051"], "description"=>"<p>Displayed are elements for which no portion was annotated. The relative age of <i>Alu</i> subfamilies increases from left to right.</p>", "links"=>[], "tags"=>["alu", "elements", "subfamilies", "annotated"], "article_id"=>378406, "categories"=>["Mathematics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["A. P. Jason de Koning", "Wanjun Gu", "Todd A. Castoe", "Mark A. Batzer", "David D. Pollock"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002384.g004", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percentage_of_Alu_elements_in_different_Alu_subfamilies_not_annotated_by_P_clouds_analysis_/378406", "title"=>"Percentage of Alu elements in different Alu subfamilies not annotated by <i>P-clouds</i> analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-01 02:20:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/708217"], "description"=>"<p>A) Predicted true distribution of <i>MIR</i> fragments in the human genome, using observed <i>RepeatMasker</i> results and <i>RepeatMasker's</i> sensitivity estimates from <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002384#pgen-1002384-g005\" target=\"_blank\">Figure 5B</a>. B) Novel <i>P</i>-clouds annotations on the RepeatMasked portion of the human genome, minus predicted false positives from dinucleotide simulations (see text).</p>", "links"=>[], "tags"=>["element-specific", "fragments"], "article_id"=>378578, "categories"=>["Mathematics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["A. P. Jason de Koning", "Wanjun Gu", "Todd A. Castoe", "Mark A. Batzer", "David D. Pollock"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002384.g006", "stats"=>{"downloads"=>3, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MIR_element_specific_P_clouds_detect_the_short_fragments_that_RepeatMasker_cannot_/378578", "title"=>"MIR element-specific <i>P-clouds</i> detect the short fragments that <i>RepeatMasker</i> cannot.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-01 02:22:58"}

PMC Usage Stats | Further Information

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