Functional annotation of the vlinc class of non-coding RNAs using systems biology approach
Identifieur interne : 003310 ( Ncbi/Curation ); précédent : 003309; suivant : 003311Functional annotation of the vlinc class of non-coding RNAs using systems biology approach
Auteurs : Georges St. Laurent [États-Unis] ; Yuri Vyatkin [États-Unis, Russie] ; Denis Antonets [Russie] ; Maxim Ri [États-Unis, Russie] ; Yao Qi [République populaire de Chine] ; Olga Saik [États-Unis, Russie] ; Dmitry Shtokalo [États-Unis, Russie] ; Michiel J. L. De Hoon [Japon] ; Hideya Kawaji [Japon] ; Masayoshi Itoh [Japon] ; Timo Lassmann [Japon, Australie] ; Erik Arner [Japon] ; Alistair R. R. Forrest [Japon] ; Estelle Nicolas [France] ; Timothy A. Mccaffrey [États-Unis] ; Piero Carninci [Japon] ; Yoshihide Hayashizaki [Japon] ; Claes Wahlestedt [États-Unis] ; Philipp Kapranov [République populaire de Chine, États-Unis]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2016.
Descripteurs français
- KwdFr :
- ARN long non codant (), ARN long non codant (génétique), ARN long non codant (métabolisme), Annotation de séquence moléculaire, Biologie des systèmes, Développement embryonnaire (génétique), Facteurs de transcription (métabolisme), Humains, Noyau de la cellule (génétique), Retroviridae (génétique), Régions promotrices (génétique), Régulation de l'expression des gènes, Séquences répétées terminales, Éléments isolateurs.
- MESH :
- génétique : ARN long non codant, Développement embryonnaire, Noyau de la cellule, Retroviridae.
- métabolisme : ARN long non codant, Facteurs de transcription.
- ARN long non codant, Annotation de séquence moléculaire, Biologie des systèmes, Humains, Régions promotrices (génétique), Régulation de l'expression des gènes, Séquences répétées terminales, Éléments isolateurs.
English descriptors
- KwdEn :
- Cell Nucleus (genetics), Embryonic Development (genetics), Gene Expression Regulation, Humans, Insulator Elements, Molecular Sequence Annotation, Promoter Regions, Genetic, RNA, Long Noncoding (classification), RNA, Long Noncoding (genetics), RNA, Long Noncoding (metabolism), Retroviridae (genetics), Systems Biology, Terminal Repeat Sequences, Transcription Factors (metabolism).
- MESH :
- chemical , classification : RNA, Long Noncoding.
- genetics : Cell Nucleus, Embryonic Development, RNA, Long Noncoding, Retroviridae.
- chemical , metabolism : RNA, Long Noncoding, Transcription Factors.
- Gene Expression Regulation, Humans, Insulator Elements, Molecular Sequence Annotation, Promoter Regions, Genetic, Systems Biology, Terminal Repeat Sequences.
Abstract
Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving this very complex aim. Here we report application of a Systems Biology-based approach to dissect functionality of a newly identified vast class of very long intergenic non-coding (vlinc) RNAs. Using highly quantitative FANTOM5 CAGE dataset, we show that these RNAs could be grouped into 1542 novel human genes based on analysis of insulators that we show here indeed function as genomic barrier elements. We show that vlincRNAs genes likely function in
Url:
DOI: 10.1093/nar/gkw162
PubMed: 27001520
PubMed Central: 4838384
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PMC:4838384Le document en format XML
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<affiliation wicri:level="1"><nlm:aff id="AFF11">Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Subiaco, 6008, Western Australia, Australia</nlm:aff>
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<author><name sortKey="Arner, Erik" sort="Arner, Erik" uniqKey="Arner E" first="Erik" last="Arner">Erik Arner</name>
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<country xml:lang="fr">Japon</country>
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<author><name sortKey="Forrest, Alistair R R" sort="Forrest, Alistair R R" uniqKey="Forrest A" first="Alistair R. R." last="Forrest">Alistair R. R. Forrest</name>
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<author><name sortKey="Nicolas, Estelle" sort="Nicolas, Estelle" uniqKey="Nicolas E" first="Estelle" last="Nicolas">Estelle Nicolas</name>
<affiliation wicri:level="1"><nlm:aff id="AFF12">LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France</nlm:aff>
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<author><name sortKey="Mccaffrey, Timothy A" sort="Mccaffrey, Timothy A" uniqKey="Mccaffrey T" first="Timothy A." last="Mccaffrey">Timothy A. Mccaffrey</name>
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<author><name sortKey="Carninci, Piero" sort="Carninci, Piero" uniqKey="Carninci P" first="Piero" last="Carninci">Piero Carninci</name>
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<affiliation wicri:level="1"><nlm:aff id="AFF9">RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
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<author><name sortKey="Hayashizaki, Yoshihide" sort="Hayashizaki, Yoshihide" uniqKey="Hayashizaki Y" first="Yoshihide" last="Hayashizaki">Yoshihide Hayashizaki</name>
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<country xml:lang="fr">Japon</country>
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<country xml:lang="fr">Japon</country>
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<wicri:noRegion>Saitama 351–0198</wicri:noRegion>
</affiliation>
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<author><name sortKey="Wahlestedt, Claes" sort="Wahlestedt, Claes" uniqKey="Wahlestedt C" first="Claes" last="Wahlestedt">Claes Wahlestedt</name>
<affiliation wicri:level="2"><nlm:aff id="AFF14">Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Ave., Miami, FL 33136, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Ave., Miami, FL 33136</wicri:regionArea>
<placeName><region type="state">Floride</region>
</placeName>
</affiliation>
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<author><name sortKey="Kapranov, Philipp" sort="Kapranov, Philipp" uniqKey="Kapranov P" first="Philipp" last="Kapranov">Philipp Kapranov</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Functional annotation of the vlinc class of non-coding RNAs using systems biology approach</title>
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<affiliation wicri:level="4"><nlm:aff id="AFF3">Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA</nlm:aff>
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<placeName><region type="state">Rhode Island</region>
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</author>
<author><name sortKey="Vyatkin, Yuri" sort="Vyatkin, Yuri" uniqKey="Vyatkin Y" first="Yuri" last="Vyatkin">Yuri Vyatkin</name>
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<country xml:lang="fr">États-Unis</country>
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</author>
<author><name sortKey="Antonets, Denis" sort="Antonets, Denis" uniqKey="Antonets D" first="Denis" last="Antonets">Denis Antonets</name>
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<affiliation wicri:level="1"><nlm:aff id="AFF5">State Research Center of Virology and Biotechnology ‘Vector’, Novosibirsk, Russia</nlm:aff>
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<affiliation wicri:level="1"><nlm:aff id="AFF6">A. P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia</nlm:aff>
<country xml:lang="fr">Russie</country>
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</affiliation>
</author>
<author><name sortKey="Ri, Maxim" sort="Ri, Maxim" uniqKey="Ri M" first="Maxim" last="Ri">Maxim Ri</name>
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<country xml:lang="fr">États-Unis</country>
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</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF4">AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia</nlm:aff>
<country xml:lang="fr">Russie</country>
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</affiliation>
</author>
<author><name sortKey="Qi, Yao" sort="Qi, Yao" uniqKey="Qi Y" first="Yao" last="Qi">Yao Qi</name>
<affiliation wicri:level="1"><nlm:aff id="AFF1">Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021</wicri:regionArea>
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</affiliation>
</author>
<author><name sortKey="Saik, Olga" sort="Saik, Olga" uniqKey="Saik O" first="Olga" last="Saik">Olga Saik</name>
<affiliation wicri:level="2"><nlm:aff id="AFF2">St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801</wicri:regionArea>
<placeName><region type="state">Massachusetts</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF4">AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia</nlm:aff>
<country xml:lang="fr">Russie</country>
<wicri:regionArea>AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090</wicri:regionArea>
<wicri:noRegion>Novosibirsk 630090</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF7">Federal Research Center Institute of Cytology and Genetics SB RAS, 10, Acad. Lavrentjev ave., Novosibirsk 630090, Russia</nlm:aff>
<country xml:lang="fr">Russie</country>
<wicri:regionArea>Federal Research Center Institute of Cytology and Genetics SB RAS, 10, Acad. Lavrentjev ave., Novosibirsk 630090</wicri:regionArea>
<wicri:noRegion>Novosibirsk 630090</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Shtokalo, Dmitry" sort="Shtokalo, Dmitry" uniqKey="Shtokalo D" first="Dmitry" last="Shtokalo">Dmitry Shtokalo</name>
<affiliation wicri:level="2"><nlm:aff id="AFF2">St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801</wicri:regionArea>
<placeName><region type="state">Massachusetts</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF4">AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia</nlm:aff>
<country xml:lang="fr">Russie</country>
<wicri:regionArea>AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090</wicri:regionArea>
<wicri:noRegion>Novosibirsk 630090</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF6">A. P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia</nlm:aff>
<country xml:lang="fr">Russie</country>
<wicri:regionArea>A. P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjev ave., Novosibirsk 630090</wicri:regionArea>
<wicri:noRegion>Novosibirsk 630090</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="De Hoon, Michiel J L" sort="De Hoon, Michiel J L" uniqKey="De Hoon M" first="Michiel J. L." last="De Hoon">Michiel J. L. De Hoon</name>
<affiliation wicri:level="1"><nlm:aff id="AFF8">RIKEN Omics Science Center (OSC)<sup>†</sup>
, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF9">RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Kawaji, Hideya" sort="Kawaji, Hideya" uniqKey="Kawaji H" first="Hideya" last="Kawaji">Hideya Kawaji</name>
<affiliation wicri:level="1"><nlm:aff id="AFF8">RIKEN Omics Science Center (OSC)<sup>†</sup>
, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF9">RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF10">RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2–1 Hirosawa, Wako-shi, Saitama 351–0198, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2–1 Hirosawa, Wako-shi, Saitama 351–0198</wicri:regionArea>
<wicri:noRegion>Saitama 351–0198</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Itoh, Masayoshi" sort="Itoh, Masayoshi" uniqKey="Itoh M" first="Masayoshi" last="Itoh">Masayoshi Itoh</name>
<affiliation wicri:level="1"><nlm:aff id="AFF8">RIKEN Omics Science Center (OSC)<sup>†</sup>
, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF9">RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF10">RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2–1 Hirosawa, Wako-shi, Saitama 351–0198, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2–1 Hirosawa, Wako-shi, Saitama 351–0198</wicri:regionArea>
<wicri:noRegion>Saitama 351–0198</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Lassmann, Timo" sort="Lassmann, Timo" uniqKey="Lassmann T" first="Timo" last="Lassmann">Timo Lassmann</name>
<affiliation wicri:level="1"><nlm:aff id="AFF8">RIKEN Omics Science Center (OSC)<sup>†</sup>
, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF9">RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF11">Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Subiaco, 6008, Western Australia, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Subiaco, 6008, Western Australia</wicri:regionArea>
<wicri:noRegion>Western Australia</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Arner, Erik" sort="Arner, Erik" uniqKey="Arner E" first="Erik" last="Arner">Erik Arner</name>
<affiliation wicri:level="1"><nlm:aff id="AFF8">RIKEN Omics Science Center (OSC)<sup>†</sup>
, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF9">RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Forrest, Alistair R R" sort="Forrest, Alistair R R" uniqKey="Forrest A" first="Alistair R. R." last="Forrest">Alistair R. R. Forrest</name>
<affiliation wicri:level="1"><nlm:aff id="AFF8">RIKEN Omics Science Center (OSC)<sup>†</sup>
, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF9">RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Nicolas, Estelle" sort="Nicolas, Estelle" uniqKey="Nicolas E" first="Estelle" last="Nicolas">Estelle Nicolas</name>
<affiliation wicri:level="1"><nlm:aff id="AFF12">LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS</wicri:regionArea>
<wicri:noRegion>UPS</wicri:noRegion>
<wicri:noRegion>UPS</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Mccaffrey, Timothy A" sort="Mccaffrey, Timothy A" uniqKey="Mccaffrey T" first="Timothy A." last="Mccaffrey">Timothy A. Mccaffrey</name>
<affiliation wicri:level="2"><nlm:aff id="AFF13">The George Washington University Medical Center, Department of Medicine, Division of Genomic Medicine, 2300 I St. NW, Washington, DC, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>The George Washington University Medical Center, Department of Medicine, Division of Genomic Medicine, 2300 I St. NW, Washington, DC</wicri:regionArea>
<placeName><region type="state">District de Columbia</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Carninci, Piero" sort="Carninci, Piero" uniqKey="Carninci P" first="Piero" last="Carninci">Piero Carninci</name>
<affiliation wicri:level="1"><nlm:aff id="AFF8">RIKEN Omics Science Center (OSC)<sup>†</sup>
, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF9">RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Hayashizaki, Yoshihide" sort="Hayashizaki, Yoshihide" uniqKey="Hayashizaki Y" first="Yoshihide" last="Hayashizaki">Yoshihide Hayashizaki</name>
<affiliation wicri:level="1"><nlm:aff id="AFF8">RIKEN Omics Science Center (OSC)<sup>†</sup>
, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>, 1–7–22 Suehiro-cho, Tsurumi-ku, Yokohama, 230–0045</wicri:regionArea>
<wicri:noRegion>230–0045</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="AFF10">RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2–1 Hirosawa, Wako-shi, Saitama 351–0198, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2–1 Hirosawa, Wako-shi, Saitama 351–0198</wicri:regionArea>
<wicri:noRegion>Saitama 351–0198</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Wahlestedt, Claes" sort="Wahlestedt, Claes" uniqKey="Wahlestedt C" first="Claes" last="Wahlestedt">Claes Wahlestedt</name>
<affiliation wicri:level="2"><nlm:aff id="AFF14">Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Ave., Miami, FL 33136, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Ave., Miami, FL 33136</wicri:regionArea>
<placeName><region type="state">Floride</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Kapranov, Philipp" sort="Kapranov, Philipp" uniqKey="Kapranov P" first="Philipp" last="Kapranov">Philipp Kapranov</name>
<affiliation wicri:level="1"><nlm:aff id="AFF1">Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021</wicri:regionArea>
<wicri:noRegion>Xiamen 361021</wicri:noRegion>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="AFF2">St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801</wicri:regionArea>
<placeName><region type="state">Massachusetts</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">Nucleic Acids Research</title>
<idno type="ISSN">0305-1048</idno>
<idno type="eISSN">1362-4962</idno>
<imprint><date when="2016">2016</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Cell Nucleus (genetics)</term>
<term>Embryonic Development (genetics)</term>
<term>Gene Expression Regulation</term>
<term>Humans</term>
<term>Insulator Elements</term>
<term>Molecular Sequence Annotation</term>
<term>Promoter Regions, Genetic</term>
<term>RNA, Long Noncoding (classification)</term>
<term>RNA, Long Noncoding (genetics)</term>
<term>RNA, Long Noncoding (metabolism)</term>
<term>Retroviridae (genetics)</term>
<term>Systems Biology</term>
<term>Terminal Repeat Sequences</term>
<term>Transcription Factors (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ARN long non codant ()</term>
<term>ARN long non codant (génétique)</term>
<term>ARN long non codant (métabolisme)</term>
<term>Annotation de séquence moléculaire</term>
<term>Biologie des systèmes</term>
<term>Développement embryonnaire (génétique)</term>
<term>Facteurs de transcription (métabolisme)</term>
<term>Humains</term>
<term>Noyau de la cellule (génétique)</term>
<term>Retroviridae (génétique)</term>
<term>Régions promotrices (génétique)</term>
<term>Régulation de l'expression des gènes</term>
<term>Séquences répétées terminales</term>
<term>Éléments isolateurs</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>RNA, Long Noncoding</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cell Nucleus</term>
<term>Embryonic Development</term>
<term>RNA, Long Noncoding</term>
<term>Retroviridae</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN long non codant</term>
<term>Développement embryonnaire</term>
<term>Noyau de la cellule</term>
<term>Retroviridae</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>RNA, Long Noncoding</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ARN long non codant</term>
<term>Facteurs de transcription</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Gene Expression Regulation</term>
<term>Humans</term>
<term>Insulator Elements</term>
<term>Molecular Sequence Annotation</term>
<term>Promoter Regions, Genetic</term>
<term>Systems Biology</term>
<term>Terminal Repeat Sequences</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>ARN long non codant</term>
<term>Annotation de séquence moléculaire</term>
<term>Biologie des systèmes</term>
<term>Humains</term>
<term>Régions promotrices (génétique)</term>
<term>Régulation de l'expression des gènes</term>
<term>Séquences répétées terminales</term>
<term>Éléments isolateurs</term>
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<front><div type="abstract" xml:lang="en"><p>Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving this very complex aim. Here we report application of a Systems Biology-based approach to dissect functionality of a newly identified vast class of very long intergenic non-coding (vlinc) RNAs. Using highly quantitative FANTOM5 CAGE dataset, we show that these RNAs could be grouped into 1542 novel human genes based on analysis of insulators that we show here indeed function as genomic barrier elements. We show that vlincRNAs genes likely function in <italic>cis</italic>
to activate nearby genes. This effect while most pronounced in closely spaced vlincRNA–gene pairs can be detected over relatively large genomic distances. Furthermore, we identified 101 vlincRNA genes likely involved in early embryogenesis based on patterns of their expression and regulation. We also found another 109 such genes potentially involved in cellular functions also happening at early stages of development such as proliferation, migration and apoptosis. Overall, we show that Systems Biology-based methods have great promise for functional annotation of non-coding RNAs.</p>
</div>
</front>
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