The Case for Junk DNA
Publication Date
May 08, 2014
Journal
PLOS Genetics
Authors
Alexander F. Palazzo & T. Ryan Gregory
Volume
10
Issue
5
Pages
e1004351
DOI
http://doi.org/10.1371/journal.pgen.1004351
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1004351
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24809441
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014423
Europe PMC
http://europepmc.org/abstract/MED/24809441
Web of Science
000337145100045
Scopus
84901596292
Mendeley
http://www.mendeley.com/research/case-junk-dna
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Mendeley | Further Information

{"title"=>"The Case for Junk DNA", "type"=>"journal", "authors"=>[{"first_name"=>"Alexander F.", "last_name"=>"Palazzo", "scopus_author_id"=>"7006400686"}, {"first_name"=>"T. Ryan", "last_name"=>"Gregory", "scopus_author_id"=>"34770258600"}], "year"=>2014, "source"=>"PLoS Genetics", "identifiers"=>{"pui"=>"373197028", "sgr"=>"84901596292", "issn"=>"15537404", "pmid"=>"24809441", "scopus"=>"2-s2.0-84901596292", "doi"=>"10.1371/journal.pgen.1004351", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)"}, "id"=>"18eb8728-c31f-330d-a0ad-078eee3b730e", "abstract"=>"With the advent of deep sequencing technologies and the ability to analyze whole genome sequences and transcrip- tomes, there has been a growing interest in exploring putative functions of the very large fraction of the genome that is commonly referred to as ‘‘junk DNA.’’ Whereas this is an issue of considerable importance in genome biology, there is an unfortunate tendency for researchers and science writers to proclaim the demise of junk DNA on a regular basis without properly addressing some of the funda- mental issues that first led to the rise of the concept. In this review, we provide an overview of the major arguments that have been presented in support of the notion that a large portion of most eukaryotic genomes lacks an organism-level function. Some of these are based on observations or basic genetic principles that are decades old, whereas others stem from new knowledge regarding molecular processes such as transcription and gene regulation.", "link"=>"http://www.mendeley.com/research/case-junk-dna", "reader_count"=>448, "reader_count_by_academic_status"=>{"Unspecified"=>7, "Professor > Associate Professor"=>29, "Researcher"=>87, "Student > Doctoral Student"=>16, "Student > Ph. D. Student"=>110, "Student > Postgraduate"=>28, "Student > Master"=>61, "Other"=>15, "Student > Bachelor"=>66, "Lecturer"=>6, "Lecturer > Senior Lecturer"=>2, "Professor"=>21}, "reader_count_by_user_role"=>{"Unspecified"=>7, "Professor > Associate Professor"=>29, "Researcher"=>87, "Student > Doctoral Student"=>16, "Student > Ph. D. Student"=>110, "Student > Postgraduate"=>28, "Student > Master"=>61, "Other"=>15, "Student > Bachelor"=>66, "Lecturer"=>6, "Lecturer > Senior Lecturer"=>2, "Professor"=>21}, "reader_count_by_subject_area"=>{"Unspecified"=>16, "Agricultural and Biological Sciences"=>281, "Arts and Humanities"=>2, "Philosophy"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Chemistry"=>3, "Computer Science"=>13, "Earth and Planetary Sciences"=>2, "Economics, Econometrics and Finance"=>1, "Engineering"=>3, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>87, "Medicine and Dentistry"=>20, "Neuroscience"=>4, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>2, "Psychology"=>2, "Social Sciences"=>3, "Immunology and Microbiology"=>3, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>20}, "Social Sciences"=>{"Social Sciences"=>3}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Psychology"=>{"Psychology"=>2}, "Unspecified"=>{"Unspecified"=>16}, "Environmental Science"=>{"Environmental Science"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>2}, "Engineering"=>{"Engineering"=>3}, "Chemistry"=>{"Chemistry"=>3}, "Neuroscience"=>{"Neuroscience"=>4}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>281}, "Computer Science"=>{"Computer Science"=>13}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>87}, "Philosophy"=>{"Philosophy"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Hungary"=>1, "United States"=>19, "United Kingdom"=>10, "Kenya"=>1, "Thailand"=>1, "Spain"=>6, "Russia"=>1, "New Zealand"=>1, "Canada"=>7, "Netherlands"=>4, "Austria"=>2, "Sweden"=>1, "Norway"=>2, "Brazil"=>8, "Denmark"=>1, "Mexico"=>2, "Israel"=>1, "France"=>5, "Chile"=>2, "Germany"=>2}, "group_count"=>14}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1490346"], "description"=>"<p>This graph is based on data for about 10,000 species <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004351#pgen.1004351-Gregory2\" target=\"_blank\">[18]</a>, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004351#pgen.1004351-Bennett1\" target=\"_blank\">[19]</a>. There is a wide range in genome sizes even among developmentally similar species, and there is no correspondence between genome size and general organism complexity. Humans, which have an average-sized genome for a mammal, are indicated by a star. Note the logarithmic scale.</p>", "links"=>[], "tags"=>["Biochemistry", "rna", "RNA processing", "RNA stability", "RNA transport", "cell biology", "Molecular cell biology", "Computational biology", "Genome evolution", "Evolutionary biology", "population genetics", "genetics", "gene expression", "DNA transcription", "Genetic elements", "Mobile genetic elements", "transposable elements", "genomics", "haploid", "dna", "contents", "groups"], "article_id"=>1020745, "categories"=>["Biological Sciences"], "users"=>["Alexander F. Palazzo", "T. Ryan Gregory"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004351.g001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_haploid_nuclear_DNA_contents_8220_genome_sizes_8221_for_various_groups_of_eukaryotes_/1020745", "title"=>"Summary of haploid nuclear DNA contents (“genome sizes”) for various groups of eukaryotes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-08 03:41:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/1490347"], "description"=>"<p>(A) Analysis of nascent and total poly(A)+ RNA levels from mouse liver nuclei. Nascent (i.e., polymerase-associated) RNA and poly(A)+ RNA were isolated from mouse liver nuclei and analyzed by high-throughput sequencing. Individual reads were categorized by their source. Exonic and intronic are from known referenced genes (i.e., “RefSeq” genes), while intergenic originate from nonreferenced loci (i.e., “non-RefSeq”) in the mouse genome. Reproduced from <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004351#pgen.1004351-Menet1\" target=\"_blank\">[85]</a>. (B) Empirical Cumulative Distribution Function (ECDF) of transcript expression in each cell compartment as determined by the ENCODE consortia. Results for RNA that either contain (“polyA+”) or lack (“polyA−”) a poly(A)-tail in the nucleus and cytosolic fractions are shown. Each human cell line that was analyzed is represented by three lines, one for each pool of RNA (red for protein-coding RNAs, blue for lncRNAs [“noncoding”], and green for intergenic transcripts [“novel intergenic”]). The lines indicate the cumulative fraction of RNAs in a given pool (y-axis) that are expressed at levels that are equal or less than the reads per kilobase per million mapped reads (RPKM) on the x-axis. Total numbers in each pool are as follows: reference protein coding genes: 20,679, loci producing lncRNAs: 9,277, and regions producing intergenic transcripts: 41,204. Transcripts with expression levels of 0 RPKM were adjusted to an artificial value of 10<sup>−6</sup> RPKM so that the onset of each graph represents the fraction of nonexpressed genes or loci. Note that 1–4 RPKM is approximately equivalent to one copy per tissue culture cell <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004351#pgen.1004351-Djebali1\" target=\"_blank\">[46]</a>, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004351#pgen.1004351-Mortazavi1\" target=\"_blank\">[129]</a>. Using this figure, one can easily deduce that the vast majority of intergenic transcripts are present at levels less than one copy per cell. Reproduced with permission from <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004351#pgen.1004351-Djebali1\" target=\"_blank\">[46]</a>.</p>", "links"=>[], "tags"=>["Biochemistry", "rna", "RNA processing", "RNA stability", "RNA transport", "cell biology", "Molecular cell biology", "Computational biology", "Genome evolution", "Evolutionary biology", "population genetics", "genetics", "gene expression", "DNA transcription", "Genetic elements", "Mobile genetic elements", "transposable elements", "genomics", "protein-coding", "intergenic", "rnas", "mammalian"], "article_id"=>1020746, "categories"=>["Biological Sciences"], "users"=>["Alexander F. Palazzo", "T. Ryan Gregory"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004351.g002", "stats"=>{"downloads"=>3, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Levels_of_protein_coding_and_intergenic_RNAs_in_mammalian_cells_/1020746", "title"=>"Levels of protein-coding and intergenic RNAs in mammalian cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-08 03:41:38"}

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