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{"title"=>"Molecular poltergeists: Mitochondrial DNA copies (numts) in sequenced nuclear genomes", "type"=>"generic", "authors"=>[{"first_name"=>"Einat", "last_name"=>"Hazkani-Covo", "scopus_author_id"=>"6506517348"}, {"first_name"=>"Raymond M.", "last_name"=>"Zeller", "scopus_author_id"=>"35789399800"}, {"first_name"=>"William", "last_name"=>"Martin", "scopus_author_id"=>"7402718622"}], "year"=>2010, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"77649210966", "doi"=>"10.1371/journal.pgen.1000834", "pui"=>"358387548", "pmid"=>"20168995", "scopus"=>"2-s2.0-77649210966", "issn"=>"15537390", "isbn"=>"1553-7404 (Electronic) 1553-7390 (Linking)"}, "id"=>"9f11e253-fd10-34bd-b028-7d68910dc5ce", "abstract"=>"The natural transfer of DNA from mitochondria to the nucleus generates nuclear copies of mitochondrial DNA (numts) and is an ongoing evolutionary process, as genome sequences attest. In humans, five different numts cause genetic disease and a dozen human loci are polymorphic for the presence of numts, underscoring the rapid rate at which mitochondrial sequences reach the nucleus over evolutionary time. In the laboratory and in nature, numts enter the nuclear DNA via non-homolgous end joining (NHEJ) at double-strand breaks (DSBs). The frequency of numt insertions among 85 sequenced eukaryotic genomes reveal that numt content is strongly correlated with genome size, suggesting that the numt insertion rate might be limited by DSB frequency. Polymorphic numts in humans link maternally inherited mitochondrial genotypes to nuclear DNA haplotypes during the past, offering new opportunities to associate nuclear markers with mitochondrial markers back in time.", "link"=>"http://www.mendeley.com/research/molecular-poltergeists-mitochondrial-dna-copies-numts-sequenced-nuclear-genomes", "reader_count"=>387, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>29, "Librarian"=>1, "Researcher"=>100, "Student > Doctoral Student"=>9, "Student > Ph. D. Student"=>108, "Student > Postgraduate"=>12, "Student > Master"=>51, "Other"=>7, "Student > Bachelor"=>41, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>3, "Professor"=>20}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>29, "Librarian"=>1, "Researcher"=>100, "Student > Doctoral Student"=>9, "Student > Ph. D. Student"=>108, "Student > Postgraduate"=>12, "Student > Master"=>51, "Other"=>7, "Student > Bachelor"=>41, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>3, "Professor"=>20}, "reader_count_by_subject_area"=>{"Unspecified"=>17, "Agricultural and Biological Sciences"=>278, "Arts and Humanities"=>2, "Veterinary Science and Veterinary Medicine"=>2, "Chemical Engineering"=>1, "Computer Science"=>10, "Earth and Planetary Sciences"=>1, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>54, "Mathematics"=>1, "Medicine and Dentistry"=>7, "Neuroscience"=>2, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Physics and Astronomy"=>2, "Social Sciences"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>7}, "Social Sciences"=>{"Social Sciences"=>3}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>17}, "Environmental Science"=>{"Environmental Science"=>5}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}, "Chemical Engineering"=>{"Chemical Engineering"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>2}, "Neuroscience"=>{"Neuroscience"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>278}, "Computer Science"=>{"Computer Science"=>10}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>54}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Colombia"=>1, "United States"=>12, "United Kingdom"=>1, "Portugal"=>2, "Switzerland"=>1, "Spain"=>1, "Canada"=>3, "Czech Republic"=>2, "Sweden"=>2, "Netherlands"=>2, "Norway"=>2, "Ireland"=>1, "Brazil"=>6, "Italy"=>3, "South Africa"=>3, "Mexico"=>1, "Australia"=>2, "Chile"=>1, "France"=>2, "Germany"=>6}, "group_count"=>17}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/863370"], "description"=>"<p>Mitochondrial DNA has been suggested to get into the nucleus via a few different pathways. (A) The most supported pathway so far involve the degradation of abnormal mitochondria <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000834#pgen.1000834-Campbell1\" target=\"_blank\">[53]</a>. Several <i>yme</i> (yeast mitochondrial escape) strains show high level of DNA escape to the nucleus. <i>yme1</i> mutant cause the inactivation of YMe1p protein, a mitochondrial-localized ATP-dependent metallo-protease leading to high escape rate of mtDNA to the nucleus. Mitochondria of <i>yme1</i> strain are taken up for degradation by the vacuole more frequently than the wild-type strain. Other pathways to get mitochondrial DNA into the nucleus were suggested including: (B) lysis of mitochondrial compartment, (C) encapsulation of mitochondrial DNA inside the nucleus, (D) direct physical association between the mitochondria and the nucleus and membrane fusions. (E) Mitochondrial DNA that enters the nucleus can integrate into nuclear chromosomes. mtDNA integrated into the chromosome during the repair of DSBs in a mechanism known as non-homologous end-joining (NHEJ). The insertion involves two DSB repair events. Each can be repaired with or without the involvement of short microhomology. In microhomology-mediated NHEJ, base-pair complements are available between the <i>numt</i> and the chromosome ends, similar to the sticky ends created by restriction enzymes.</p>", "links"=>[], "tags"=>["Evolutionary biology", "genetics and genomics/comparative genomics"], "article_id"=>533831, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Einat Hazkani-Covo", "Raymond M. Zeller", "William Martin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000834.g004", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mechanism_of_numt_insertion_/533831", "title"=>"Mechanism of <i>numt</i> insertion.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:41:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/863256"], "description"=>"<p>A log–log scale graph showing the dependency between <i>numt</i> content in genomes and genome size. Information regarding genome size is from <a href=\"http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi\" target=\"_blank\">http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi</a>.</p>", "links"=>[], "tags"=>["correlated", "genome"], "article_id"=>533719, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Einat Hazkani-Covo", "Raymond M. Zeller", "William Martin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000834.g003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Numt_content_is_correlated_to_genome_size_/533719", "title"=>"<i>Numt</i> content is correlated to genome size.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:40:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/863173"], "description"=>"<p>Human mitochondrial DNA (NC_001807) is shown in the inner circle, and <i>numt</i> insertions are shown in the outer circle. Polymorphic <i>numts</i> are shown in light green (<i>numts</i> exist in the reference genome) or dark green (<i>numts</i> are missing from the reference genome). <i>Numts</i> causing disease are shown in red. In each case, the reference and the SNP accession numbers (if available) are given. When a <i>numt</i> is inserted within gene, the gene name is indicated (green and red ellipses for polymorphic <i>numts</i> and for <i>numts</i> causing disease, respectively).</p>", "links"=>[], "tags"=>["polymorphic"], "article_id"=>533636, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Einat Hazkani-Covo", "Raymond M. Zeller", "William Martin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000834.g002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Human_polymorphic_numts_and_numts_that_cause_diseases_/533636", "title"=>"Human polymorphic <i>numts</i> and <i>numts</i> that cause diseases.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:40:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/863473"], "description"=>"<p>For each organism the number of BLAST hits as well as the unique number of bases in genomes is given (i.e. a base in the genome that has a BLAST hit to two repetitive mitochondria pieces it is count only once in <i>numt</i> content). Other available <i>numt</i> estimates are indicated with their references, where the corresponding search parameters are given.</p>", "links"=>[], "tags"=>["85", "mitochondria", "genomes"], "article_id"=>533930, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Einat Hazkani-Covo", "Raymond M. Zeller", "William Martin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000834.t001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Blast_analysis_of_85_mitochondria_against_their_nuclear_genomes_BlastN_e_score_8202_8202_0_0001_/533930", "title"=>"Blast analysis of 85 mitochondria against their nuclear genomes (BlastN, e-score = 0.0001).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 02:42:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/863093"], "description"=>"<p>(A) Dating <i>numt</i> insertion based on a mitochondrial phylogenetic tree (black branches). An arrow indicates time of insertion and the <i>numt</i> branch is shown in red. The methodology can be used only in species where the mitochondrial rate of evolution is lower than the nuclear rate of evolution (e.g., mammals but not plants) and when the <i>numts</i> are long enough (>1 kb) to carry enough evolutionary signal. (B) Dating <i>numt</i> insertion based on patterns of presence and absence on a phylogeny. Few nuclear genomes and their genome alignment are used to identify <i>numt</i> insertions. Species that share the descendant from the common ancestor where the transfer occurred include the <i>numts</i> (red rectangle) whereas this <i>numt</i> is missing in the others.</p>", "links"=>[], "tags"=>["Evolutionary biology", "genetics and genomics/comparative genomics"], "article_id"=>533551, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Einat Hazkani-Covo", "Raymond M. Zeller", "William Martin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000834.g001", "stats"=>{"downloads"=>1, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dating_numt_insertion_/533551", "title"=>"Dating <i>numt</i> insertion.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:39:58"}

PMC Usage Stats | Further Information

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