The Genetic Signatures of Noncoding RNAs
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{"title"=>"The genetic signatures of noncoding RNAs", "type"=>"generic", "authors"=>[{"first_name"=>"John S.", "last_name"=>"Mattick", "scopus_author_id"=>"7005637143"}], "year"=>2009, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"65649092633", "doi"=>"10.1371/journal.pgen.1000459", "pui"=>"354669612", "pmid"=>"19390609", "scopus"=>"2-s2.0-65649092633", "issn"=>"15537390", "isbn"=>"10.1371/journal.pgen.1000459", "arxiv"=>"NIHMS150003"}, "id"=>"c36c8bdc-e3fd-3f21-b59b-67f8183aa0e6", "abstract"=>"The majority of the genome in animals and plants is transcribed in a developmentally regulated manner to produce large numbers of non-protein-coding RNAs (ncRNAs), whose incidence increases with developmental complexity. There is growing evidence that these transcripts are functional, particularly in the regulation of epigenetic processes, leading to the suggestion that they compose a hitherto hidden layer of genomic programming in humans and other complex organisms. However, to date, very few have been identified in genetic screens. Here I show that this is explicable by an historic emphasis, both phenotypically and technically, on mutations in protein-coding sequences, and by presumptions about the nature of regulatory mutations. Most variations in regulatory sequences produce relatively subtle phenotypic changes, in contrast to mutations in protein-coding sequences that frequently cause catastrophic component failure. Until recently, most mapping projects have focused on protein-coding sequences, and the limited number of identified regulatory mutations have been interpreted as affecting conventional cis-acting promoter and enhancer elements, although these regions are often themselves transcribed. Moreover, ncRNA-directed regulatory circuits underpin most, if not all, complex genetic phenomena in eukaryotes, including RNA interference-related processes such as transcriptional and post-transcriptional gene silencing, position effect variegation, hybrid dysgenesis, chromosome dosage compensation, parental imprinting and allelic exclusion, paramutation, and possibly transvection and transinduction. The next frontier is the identification and functional characterization of the myriad sequence variations that influence quantitative traits, disease susceptibility, and other complex characteristics, which are being shown by genome-wide association studies to lie mostly in noncoding, presumably regulatory, regions. There is every possibility that many of these variations will alter the interactions between regulatory RNAs and their targets, a prospect that should be borne in mind in future functional analyses.", "link"=>"http://www.mendeley.com/research/genetic-signatures-noncoding-rnas-5", "reader_count"=>264, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>21, "Librarian"=>1, "Researcher"=>81, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>80, "Student > Postgraduate"=>7, "Student > Master"=>32, "Other"=>5, "Student > Bachelor"=>12, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>10}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>21, "Librarian"=>1, "Researcher"=>81, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>80, "Student > Postgraduate"=>7, "Student > Master"=>32, "Other"=>5, "Student > Bachelor"=>12, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>10}, "reader_count_by_subject_area"=>{"Unspecified"=>9, "Biochemistry, Genetics and Molecular Biology"=>42, "Mathematics"=>1, "Agricultural and Biological Sciences"=>186, "Medicine and Dentistry"=>12, "Arts and Humanities"=>1, "Neuroscience"=>2, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Physics and Astronomy"=>1, "Social Sciences"=>2, "Computer Science"=>4, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>12}, "Neuroscience"=>{"Neuroscience"=>2}, "Social Sciences"=>{"Social Sciences"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>186}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>42}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>9}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "Argentina"=>1, "United States"=>11, "Japan"=>1, "United Kingdom"=>1, "Portugal"=>1, "Spain"=>2, "Russia"=>2, "Canada"=>1, "Sweden"=>2, "Netherlands"=>1, "Belgium"=>2, "Norway"=>1, "Luxembourg"=>1, "China"=>1, "Brazil"=>5, "Denmark"=>1, "Italy"=>4, "Australia"=>1, "France"=>1, "Chile"=>2, "Germany"=>2}, "group_count"=>10}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/900422"], "description"=>"<p>The number of indexed Medline entries with the words “non-coding RNA”, “noncoding RNA”, “non-protein-coding RNA” or “ncRNA” in the title, abstract or keywords is plotted per year. Data courtesy of Ryan J. Taft.</p>", "links"=>[], "tags"=>["papers"], "article_id"=>570904, "categories"=>["Genetics"], "users"=>["John S. Mattick"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000459.g001", "stats"=>{"downloads"=>4, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_recent_rise_in_papers_on_ncRNAs_/570904", "title"=>"The recent rise in papers on ncRNAs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 06:09:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/900545"], "description"=>"<p>Indices of the functionality of ncRNAs.</p>", "links"=>[], "tags"=>["functionality"], "article_id"=>571005, "categories"=>["Genetics"], "users"=>["John S. Mattick"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000459.t002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Indices_of_the_functionality_of_ncRNAs_/571005", "title"=>"Indices of the functionality of ncRNAs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 06:10:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/900487"], "description"=>"<p>A conceptual diagram of the spectrum of phenotypic effects of mutations in sequences encoding proteins and other analogue components of cells (continuous line) versus variations in non-coding sequences that specify regulatory interactions (dashed line).</p>", "links"=>[], "tags"=>["contrasting", "mutations", "protein-coding"], "article_id"=>570948, "categories"=>["Genetics"], "users"=>["John S. Mattick"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000459.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_contrasting_effects_of_mutations_in_protein_coding_and_regulatory_sequences_/570948", "title"=>"The contrasting effects of mutations in protein-coding and regulatory sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 06:10:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/900571"], "description"=>"<p>This list is not exhaustive, and there are other examples of functional ncRNAs in mammals (see e.g. <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000459#pgen.1000459-Katayama1\" target=\"_blank\">[228]</a>) as well as of regulatory and structural ncRNAs in other animals, plants, fungi (see e.g. <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000459#pgen.1000459-Rajendra1\" target=\"_blank\">[6]</a>–<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000459#pgen.1000459-Camblong1\" target=\"_blank\">[11]</a>) and bacteria <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000459#pgen.1000459-ToledoArana1\" target=\"_blank\">[229]</a>.</p>a<p>Abbreviations used are: siRNA, short interfering RNA; shRNA, short hairpin RNA; FISH, fluorescence in situ hybridization; ChIP, chromatin immunoprecipitation; RNA-IP, immunoprecipitation of RNA associated with particular proteins.</p>", "links"=>[], "tags"=>["mammalian", "noncoding"], "article_id"=>571037, "categories"=>["Genetics"], "users"=>["John S. Mattick"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000459.t001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_functional_mammalian_noncoding_RNAs_/571037", "title"=>"Examples of functional mammalian noncoding RNAs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 06:10:45"}

PMC Usage Stats | Further Information

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