Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding RNAs
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{"title"=>"Clusters of internally primed transcripts reveal novel long noncoding RNAs", "type"=>"generic", "authors"=>[{"first_name"=>"Masaaki", "last_name"=>"Furuno", "scopus_author_id"=>"7004634550"}, {"first_name"=>"Ken C.", "last_name"=>"Pang", "scopus_author_id"=>"7101856056"}, {"first_name"=>"Noriko", "last_name"=>"Ninomiya", "scopus_author_id"=>"7004117331"}, {"first_name"=>"Shiro", "last_name"=>"Fukuda", "scopus_author_id"=>"46261142300"}, {"first_name"=>"Martin C.", "last_name"=>"Frith", "scopus_author_id"=>"13407194500"}, {"first_name"=>"Carol", "last_name"=>"Bult", "scopus_author_id"=>"6701467886"}, {"first_name"=>"Chikatoshi", "last_name"=>"Kai", "scopus_author_id"=>"7006157038"}, {"first_name"=>"Jun", "last_name"=>"Kawai", "scopus_author_id"=>"9268980900"}, {"first_name"=>"Piero", "last_name"=>"Carninci", "scopus_author_id"=>"7005203099"}, {"first_name"=>"Yoshihide", "last_name"=>"Hayashizaki", "scopus_author_id"=>"35355246400"}, {"first_name"=>"John S.", "last_name"=>"Mattick", "scopus_author_id"=>"7005637143"}, {"first_name"=>"Harukazu", "last_name"=>"Suzuki", "scopus_author_id"=>"7406835659"}], "year"=>2006, "source"=>"PLoS Genetics", "identifiers"=>{"pui"=>"43696017", "isbn"=>"1553-7404 (Electronic)", "sgr"=>"33646474262", "issn"=>"15537390", "pmid"=>"16683026", "scopus"=>"2-s2.0-33646474262", "doi"=>"10.1371/journal.pgen.0020037"}, "id"=>"6a557706-e230-31af-ac01-1d81db7f6e6e", "abstract"=>"Non-protein-coding RNAs (ncRNAs) are increasingly being recognized as having important regulatory roles. Although much recent attention has focused on tiny 22- to 25-nucleotide microRNAs, several functional ncRNAs are orders of magnitude larger in size. Examples of such macro ncRNAs include Xist and Air, which in mouse are 18 and 108 kilobases (Kb), respectively. We surveyed the 102,801 FANTOM3 mouse cDNA clones and found that Air and Xist were present not as single, full-length transcripts but as a cluster of multiple, shorter cDNAs, which were unspliced, had little coding potential, and were most likely primed from internal adenine-rich regions within longer parental transcripts. We therefore conducted a genome-wide search for regional clusters of such cDNAs to find novel macro ncRNA candidates. Sixty-six regions were identified, each of which mapped outside known protein-coding loci and which had a mean length of 92 Kb. We detected several known long ncRNAs within these regions, supporting the basic rationale of our approach. In silico analysis showed that many regions had evidence of imprinting and/or antisense transcription. These regions were significantly associated with microRNAs and transcripts from the central nervous system. We selected eight novel regions for experimental validation by northern blot and RT-PCR and found that the majority represent previously unrecognized noncoding transcripts that are at least 10 Kb in size and predominantly localized in the nucleus. Taken together, the data not only identify multiple new ncRNAs but also suggest the existence of many more macro ncRNAs like Xist and Air.", "link"=>"http://www.mendeley.com/research/clusters-internally-primed-transcripts-reveal-novel-long-noncoding-rnas", "reader_count"=>135, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>14, "Librarian"=>1, "Researcher"=>47, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>28, "Student > Postgraduate"=>5, "Student > Master"=>10, "Other"=>4, "Student > Bachelor"=>5, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>11}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>14, "Librarian"=>1, "Researcher"=>47, "Student > Doctoral Student"=>4, "Student > Ph. D. 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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/959389"], "description"=>"<p>FANTOM and public transcripts were clustered into 37,348 TUs by grouping\n\t\t\t\t\t\t\tany two or more transcripts that shared genomic coordinates. Then, the\n\t\t\t\t\t\t\tfollowing procedures were applied. (1) Protein-coding TUs were excluded\n\t\t\t\t\t\t\tby removing any whose transcripts had an open reading frame of either\n\t\t\t\t\t\t\t150 amino acids or more (RIKEN/MGC cDNAs) or one amino acid or more\n\t\t\t\t\t\t\t(non-RIKEN/MGC cDNAs). (2) TUs wholly encompassed within introns of\n\t\t\t\t\t\t\tprotein-coding TUs were excluded to avoid possible pre-mRNA intronic\n\t\t\t\t\t\t\ttranscripts. (3) Intron-containing TUs were excluded to select for\n\t\t\t\t\t\t\tunspliced transcripts. (4) TUs lacking adjunct adenine-rich regions or\n\t\t\t\t\t\t\tcontaining polyA signals were excluded to select for internally primed\n\t\t\t\t\t\t\ttranscripts. (5) Remaining UNA TUs that mapped within 100 Kb of one\n\t\t\t\t\t\t\tanother on the mouse genome (mm5) were clustered together, provided they\n\t\t\t\t\t\t\tdid not overlap the genomic coordinates of a protein-coding TU/NCBI\n\t\t\t\t\t\t\tRefSeq/Ensembl gene model with a CDS of 150 amino acids or more or a\n\t\t\t\t\t\t\tnoncoding TU with a polyA signal within 100 bp of the 3′ end and without\n\t\t\t\t\t\t\tan adjunct adenine-rich region. (6) Reliably expressed UNA TU clusters\n\t\t\t\t\t\t\twere selected by identifying those with at least ten supporting ESTs.\n\t\t\t\t\t\t\t(7) Selected UNA TU clusters were then manually screened and separated\n\t\t\t\t\t\t\tbased upon evidence of possible internal transcription state sites\n\t\t\t\t\t\t\t(based upon CpG islands, CAGE tags, and EST clusters), resulting in the\n\t\t\t\t\t\t\tidentification of 66 ENORs.</p>", "links"=>[], "tags"=>["pipeline"], "article_id"=>629410, "categories"=>["Genetics", "Biotechnology", "Biological Sciences", "Molecular Biology", "Evolutionary Biology"], "users"=>["Masaaki Furuno", "Ken C Pang", "Noriko Ninomiya", "Shiro Fukuda", "Martin C Frith", "Carol Bult", "Chikatoshi Kai", "Jun Kawai", "Piero Carninci", "Yoshihide Hayashizaki", "John S Mattick", "Harukazu Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020037.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Discovery_Pipeline_for_ENORs_/629410", "title"=>"Discovery Pipeline for ENORs", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:42:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/959260"], "description"=>"<div><p>(A) The <i>Air</i>/<i>Igf2r</i> locus (Chromosome 17:\n\t\t\t\t\t\t\t12,091,531–12,258,195).</p>\n\t\t\t\t\t\t<p>(B) The <i>Xist</i>/<i>Tsix</i> locus (X chromosome:\n\t\t\t\t\t\t\t94,835,096–94,888,536).</p>\n\t\t\t\t\t\t<p>(C) The dystrophin <i>(Dmd)</i> locus (X chromosome:\n\t\t\t\t\t\t\t76,500,000–76,754,601).</p>\n\t\t\t\t\t\t<p>For the transcripts, cDNA sequences from the RIKEN and public databases\n\t\t\t\t\t\t\tare shown, and are colored in brown and purple depending upon their\n\t\t\t\t\t\t\tchromosomal strand of origin. Predicted genes from Ensembl, NCBI, and\n\t\t\t\t\t\t\tRefSeq databases are shown in gray. CpG islands as defined by the UCSC\n\t\t\t\t\t\t\tGenome Browser are shown. Blue circles indicate unspliced, noncoding\n\t\t\t\t\t\t\tRIKEN cDNAs with adjunct adenine-rich regions. Red circles indicate\n\t\t\t\t\t\t\tRIKEN imprinted cDNA candidates [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020037#pgen-0020037-b038\" target=\"_blank\">38</a>].</p></div>", "links"=>[], "tags"=>["gev"], "article_id"=>629285, "categories"=>["Genetics", "Biotechnology", "Biological Sciences", "Molecular Biology", "Evolutionary Biology"], "users"=>["Masaaki Furuno", "Ken C Pang", "Noriko Ninomiya", "Shiro Fukuda", "Martin C Frith", "Carol Bult", "Chikatoshi Kai", "Jun Kawai", "Piero Carninci", "Yoshihide Hayashizaki", "John S Mattick", "Harukazu Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020037.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Snapshots_of_the_GEV_Showing_Transcription_/629285", "title"=>"Snapshots of the GEV Showing Transcription", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:41:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/959922"], "description"=>"<p>qRT-PCR was carried out using total and cytoplasmic RNA from mouse whole\n\t\t\t\t\t\t\tbrain and the corresponding primer pairs (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020037#pgen-0020037-st003\" target=\"_blank\">Table\n\t\t\t\t\t\t\t\tS3</a>). ENORs are listed in increasing order based on the\n\t\t\t\t\t\t\testimated length of each region. Apart from the results shown, we also\n\t\t\t\t\t\t\texamined the localization of other mRNAs <i>(β-actin</i> and\n\t\t\t\t\t\t\t\t<i>GAPDH)</i> and additional regions of\n\t\t\t\t\t\t\t\t<i>Rian</i> and other ENORs, and these results were\n\t\t\t\t\t\t\tconsistent with the rest (unpublished data).</p>", "links"=>[], "tags"=>["enor"], "article_id"=>629932, "categories"=>["Genetics", "Biotechnology", "Biological Sciences", "Molecular Biology", "Evolutionary Biology"], "users"=>["Masaaki Furuno", "Ken C Pang", "Noriko Ninomiya", "Shiro Fukuda", "Martin C Frith", "Carol Bult", "Chikatoshi Kai", "Jun Kawai", "Piero Carninci", "Yoshihide Hayashizaki", "John S Mattick", "Harukazu Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020037.g007", "stats"=>{"downloads"=>3, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Localization_of_ENOR_Transcripts_/629932", "title"=>"Localization of ENOR Transcripts", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:46:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/959540"], "description"=>"<p>Tissue expression information for individual ENORs was obtained using\n\t\t\t\t\t\t\tpublicly available GNF Gene Expression Atlas data. GNF probes that\n\t\t\t\t\t\t\toverlapped ENORs were identified, and the corresponding relative\n\t\t\t\t\t\t\texpression ratios for 61 tissues were hierarchically clustered. Red\n\t\t\t\t\t\t\tsquares indicate high expression, black squares indicate low expression,\n\t\t\t\t\t\t\tand grey squares indicate where expression was not reliably detected\n\t\t\t\t\t\t\t(based upon Affymetrix MAS5 absent/present calls). med. olfactory epi.,\n\t\t\t\t\t\t\tmedial olfactory epithelium.</p>", "links"=>[], "tags"=>["Computational biology", "biotechnology", "Evolutionary biology", "molecular biology", "genetics and genomics/gene expression"], "article_id"=>629553, "categories"=>["Genetics", "Biotechnology", "Biological Sciences", "Molecular Biology", "Evolutionary Biology"], "users"=>["Masaaki Furuno", "Ken C Pang", "Noriko Ninomiya", "Shiro Fukuda", "Martin C Frith", "Carol Bult", "Chikatoshi Kai", "Jun Kawai", "Piero Carninci", "Yoshihide Hayashizaki", "John S Mattick", "Harukazu Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020037.g003", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ENOR_Tissue_Expression_/629553", "title"=>"ENOR Tissue Expression", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:43:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/471416", "https://ndownloader.figshare.com/files/471508", "https://ndownloader.figshare.com/files/471597", "https://ndownloader.figshare.com/files/471617", "https://ndownloader.figshare.com/files/471645", "https://ndownloader.figshare.com/files/471668"], "description"=>"<div><p>Non-protein-coding RNAs (ncRNAs) are increasingly being recognized as having important regulatory roles. Although much recent attention has focused on tiny 22- to 25-nucleotide microRNAs, several functional ncRNAs are orders of magnitude larger in size. Examples of such macro ncRNAs include <em>Xist</em> and <em>Air,</em> which in mouse are 18 and 108 kilobases (Kb), respectively. We surveyed the 102,801 FANTOM3 mouse cDNA clones and found that <em>Air</em> and <em>Xist</em> were present not as single, full-length transcripts but as a cluster of multiple, shorter cDNAs, which were unspliced, had little coding potential, and were most likely primed from internal adenine-rich regions within longer parental transcripts. We therefore conducted a genome-wide search for regional clusters of such cDNAs to find novel macro ncRNA candidates. Sixty-six regions were identified, each of which mapped outside known protein-coding loci and which had a mean length of 92 Kb. We detected several known long ncRNAs within these regions, supporting the basic rationale of our approach. In silico analysis showed that many regions had evidence of imprinting and/or antisense transcription. These regions were significantly associated with microRNAs and transcripts from the central nervous system. We selected eight novel regions for experimental validation by northern blot and RT-PCR and found that the majority represent previously unrecognized noncoding transcripts that are at least 10 Kb in size and predominantly localized in the nucleus. Taken together, the data not only identify multiple new ncRNAs but also suggest the existence of many more macro ncRNAs like <em>Xist</em> and <em>Air</em>.</p> </div>", "links"=>[], "tags"=>["clusters", "internally", "primed", "transcripts"], "article_id"=>152949, "categories"=>["Genetics", "Biotechnology", "Biological Sciences", "Molecular Biology", "Evolutionary Biology"], "users"=>["Masaaki Furuno", "Ken C Pang", "Noriko Ninomiya", "Shiro Fukuda", "Martin C Frith", "Carol Bult", "Chikatoshi Kai", "Jun Kawai", "Piero Carninci", "Yoshihide Hayashizaki", "John S Mattick", "Harukazu Suzuki"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.0020037.sg001", "https://dx.doi.org/10.1371/journal.pgen.0020037.sg002", "https://dx.doi.org/10.1371/journal.pgen.0020037.st001", "https://dx.doi.org/10.1371/journal.pgen.0020037.st002", "https://dx.doi.org/10.1371/journal.pgen.0020037.st003", "https://dx.doi.org/10.1371/journal.pgen.0020037.st004"], "stats"=>{"downloads"=>12, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Clusters_of_Internally_Primed_Transcripts_Reveal_Novel_Long_Noncoding_RNAs/152949", "title"=>"Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding\n\t\t\t\t\tRNAs", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2006-04-28 00:49:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/959741"], "description"=>"<p>PCR was carried out with and without reverse transcription (RT[+] and\n\t\t\t\t\t\t\tRT[−], respectively) using midbrain total RNA and the corresponding\n\t\t\t\t\t\t\tprimer pairs (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020037#pgen-0020037-st003\" target=\"_blank\">Table S3</a>). PCR using genomic DNA was\n\t\t\t\t\t\t\talso carried out as a control. A DNA ladder (Promega; <a href=\"http://www.promega.com\" target=\"_blank\">http://www.promega.com</a>) was used as a\n\t\t\t\t\t\t\tsize marker. The amplified fragments were confirmed as the expected ones\n\t\t\t\t\t\t\tby analyzing digestion pattern using several restriction enzymes. The\n\t\t\t\t\t\t\tlower band, observed in the RT(+) lane of the amplified fragment C,\n\t\t\t\t\t\t\tseems to be nonspecific, because it was amplified using only the right\n\t\t\t\t\t\t\tprimer and because it showed a digestion pattern with restriction\n\t\t\t\t\t\t\tenzymes quite different from that of the upper band and the band of the\n\t\t\t\t\t\t\tgenomic DNA (unpublished data).</p>", "links"=>[], "tags"=>["transcription", "adjacent"], "article_id"=>629759, "categories"=>["Genetics", "Biotechnology", "Biological Sciences", "Molecular Biology", "Evolutionary Biology"], "users"=>["Masaaki Furuno", "Ken C Pang", "Noriko Ninomiya", "Shiro Fukuda", "Martin C Frith", "Carol Bult", "Chikatoshi Kai", "Jun Kawai", "Piero Carninci", "Yoshihide Hayashizaki", "John S Mattick", "Harukazu Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020037.g005", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Presence_of_Transcription_between_Adjacent_cDNAs_/629759", "title"=>"Presence of Transcription between Adjacent cDNAs", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:44:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/959837"], "description"=>"<p>Mouse whole brain total RNA (10 μg/lane) was used for the analysis except\n\t\t\t\t\t\t\tfor ENOR2 and ENOR61, where mouse thymus total RNA was used. DNA\n\t\t\t\t\t\t\tfragments without any predicted repeated sequences were PCR-amplified\n\t\t\t\t\t\t\tfrom cDNAs in ENORs (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020037#pgen-0020037-st003\" target=\"_blank\">Table S3</a>), labeled with\n\t\t\t\t\t\t\t\t<sup>32</sup>P-dCTP (Amersham Biosciences), and then used as probes.\n\t\t\t\t\t\t\tRNA size was estimated with an RNA ladder (Invitrogen). ENORs are listed\n\t\t\t\t\t\t\tin increasing order based on the estimated length of each region.</p>", "links"=>[], "tags"=>["blot", "enor"], "article_id"=>629852, "categories"=>["Genetics", "Biotechnology", "Biological Sciences", "Molecular Biology", "Evolutionary Biology"], "users"=>["Masaaki Furuno", "Ken C Pang", "Noriko Ninomiya", "Shiro Fukuda", "Martin C Frith", "Carol Bult", "Chikatoshi Kai", "Jun Kawai", "Piero Carninci", "Yoshihide Hayashizaki", "John S Mattick", "Harukazu Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020037.g006", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Northern_Blot_Analysis_of_ENOR_Transcripts_/629852", "title"=>"Northern Blot Analysis of ENOR Transcripts", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:45:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/959651"], "description"=>"<p>Analysis of (A) <i>Air,</i> (B) ENOR28, and (C) ENOR31 loci.\n\t\t\t\t\t\t\tAbove in each panel, screen shots of the GEV featuring the loci around\n\t\t\t\t\t\t\t\t<i>Air,</i> ENOR28, and ENOR31 are shown. The orange bars\n\t\t\t\t\t\t\tindicate the regions for <i>Air,</i> ENOR28, and ENOR31. cDNA\n\t\t\t\t\t\t\tsequences from the RIKEN and public databases are shown. Sequences\n\t\t\t\t\t\t\tmapped on the plus strand and minus strand are brown and purple,\n\t\t\t\t\t\t\trespectively. Predicted genes from Ensembl, NCBI, and RefSeq databases\n\t\t\t\t\t\t\tare shown in gray. For RIKEN imprinted transcripts, imprinted cDNA\n\t\t\t\t\t\t\tcandidates identified previously [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020037#pgen-0020037-b038\" target=\"_blank\">38</a>] are shown. CpG islands as defined\n\t\t\t\t\t\t\tby the UCSC Genome Browser are shown. Positions of primer pairs are\n\t\t\t\t\t\t\tmarked by small vertical arrows. Below in each panel, qRT-PCR results\n\t\t\t\t\t\t\tfor midbrain, hippocampus, thalamus, striatum, and testis using the\n\t\t\t\t\t\t\tcorresponding primer pairs are shown.</p>", "links"=>[], "tags"=>["Computational biology", "biotechnology", "Evolutionary biology", "molecular biology", "genetics and genomics/gene expression"], "article_id"=>629663, "categories"=>["Genetics", "Biotechnology", "Biological Sciences", "Molecular Biology", "Evolutionary Biology"], "users"=>["Masaaki Furuno", "Ken C Pang", "Noriko Ninomiya", "Shiro Fukuda", "Martin C Frith", "Carol Bult", "Chikatoshi Kai", "Jun Kawai", "Piero Carninci", "Yoshihide Hayashizaki", "John S Mattick", "Harukazu Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020037.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_qRT_PCR_Analysis_/629663", "title"=>"qRT-PCR Analysis", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:44:13"}

PMC Usage Stats | Further Information

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Relative Metric

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