AustralieFrV1, PubMed, Curation, bibRecord, 002019

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

Identifieur interne : 002019 ( PubMed/Curation ); précédent : 002018; suivant : 002020

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

Auteurs : Georges St Laurent [États-Unis] ; Yuri Vyatkin [Russie] ; Denis Antonets [Russie] ; Maxim Ri [Russie] ; Yao Qi [République populaire de Chine] ; Olga Saik [Russie] ; Dmitry Shtokalo [Russie] ; Michiel J L. De Hoon [Japon] ; Hideya Kawaji [Japon] ; Masayoshi Itoh [Japon] ; Timo Lassmann [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 [Oman] ; Philipp Kapranov [Oman]

Source :

Nucleic acids research [ 1362-4962 ] ; 2016.

RBID : pubmed:27001520

Descripteurs français

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 vlinc RNAs genes likely function in cisto activate nearby genes. This effect while most pronounced in closely spaced vlinc RNA-gene pairs can be detected over relatively large genomic distances. Furthermore, we identified 101 vlinc RNA 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.

DOI: 10.1093/nar/gkw162
PubMed: 27001520

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<author><name sortKey="St Laurent, Georges" sort="St Laurent, Georges" uniqKey="St Laurent G" first="Georges" last="St Laurent">Georges St Laurent</name>
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<author><name sortKey="Vyatkin, Yuri" sort="Vyatkin, Yuri" uniqKey="Vyatkin Y" first="Yuri" last="Vyatkin">Yuri Vyatkin</name>
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<author><name sortKey="Qi, Yao" sort="Qi, Yao" uniqKey="Qi Y" first="Yao" last="Qi">Yao Qi</name>
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<author><name sortKey="Shtokalo, Dmitry" sort="Shtokalo, Dmitry" uniqKey="Shtokalo D" first="Dmitry" last="Shtokalo">Dmitry Shtokalo</name>
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<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>
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<author><name sortKey="Kawaji, Hideya" sort="Kawaji, Hideya" uniqKey="Kawaji H" first="Hideya" last="Kawaji">Hideya Kawaji</name>
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<author><name sortKey="Itoh, Masayoshi" sort="Itoh, Masayoshi" uniqKey="Itoh M" first="Masayoshi" last="Itoh">Masayoshi Itoh</name>
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<author><name sortKey="Lassmann, Timo" sort="Lassmann, Timo" uniqKey="Lassmann T" first="Timo" last="Lassmann">Timo Lassmann</name>
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<country xml:lang="fr">Australie</country>
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</author>
<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>
<wicri:regionArea>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045</wicri:regionArea>
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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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<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045</wicri:regionArea>
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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:affiliation>LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
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</affiliation>
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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>
<affiliation wicri:level="1"><nlm:affiliation>The George Washington University Medical Center, Department of Medicine, Division of Genomic Medicine, 2300 I St. NW, Washington, DC, USA.</nlm:affiliation>
<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>
</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:affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045</wicri:regionArea>
</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:affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama 351-0198</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Wahlestedt, Claes" sort="Wahlestedt, Claes" uniqKey="Wahlestedt C" first="Claes" last="Wahlestedt">Claes Wahlestedt</name>
<affiliation wicri:level="1"><nlm:affiliation>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 clawah@gmail.com.</nlm:affiliation>
<country wicri:rule="url">Oman</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>
</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:affiliation>Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA philippk08@hotmail.com.</nlm:affiliation>
<country wicri:rule="url">Oman</country>
<wicri:regionArea>Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801</wicri:regionArea>
</affiliation>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.</title>
<author><name sortKey="St Laurent, Georges" sort="St Laurent, Georges" uniqKey="St Laurent G" first="Georges" last="St Laurent">Georges St Laurent</name>
<affiliation wicri:level="1"><nlm:affiliation>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Vyatkin, Yuri" sort="Vyatkin, Yuri" uniqKey="Vyatkin Y" first="Yuri" last="Vyatkin">Yuri Vyatkin</name>
<affiliation wicri:level="1"><nlm:affiliation>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia.</nlm:affiliation>
<country xml:lang="fr">Russie</country>
<wicri:regionArea>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Antonets, Denis" sort="Antonets, Denis" uniqKey="Antonets D" first="Denis" last="Antonets">Denis Antonets</name>
<affiliation wicri:level="1"><nlm:affiliation>AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia State Research Center of Virology and Biotechnology 'Vector', Novosibirsk, Russia A. P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia.</nlm:affiliation>
<country xml:lang="fr">Russie</country>
<wicri:regionArea>AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia State Research Center of Virology and Biotechnology 'Vector', Novosibirsk, Russia A. P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjev ave., Novosibirsk 630090</wicri:regionArea>
</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">Russie</country>
<wicri:regionArea>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090</wicri:regionArea>
</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:affiliation>Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China.</nlm:affiliation>
<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>
</affiliation>
</author>
<author><name sortKey="Saik, Olga" sort="Saik, Olga" uniqKey="Saik O" first="Olga" last="Saik">Olga Saik</name>
<affiliation wicri:level="1"><nlm:affiliation>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia Federal Research Center Institute of Cytology and Genetics SB RAS, 10, Acad. Lavrentjev ave., Novosibirsk 630090, Russia.</nlm:affiliation>
<country xml:lang="fr">Russie</country>
<wicri:regionArea>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia Federal Research Center Institute of Cytology and Genetics SB RAS, 10, Acad. Lavrentjev ave., Novosibirsk 630090</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Shtokalo, Dmitry" sort="Shtokalo, Dmitry" uniqKey="Shtokalo D" first="Dmitry" last="Shtokalo">Dmitry Shtokalo</name>
<affiliation wicri:level="1"><nlm:affiliation>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia A. P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia.</nlm:affiliation>
<country xml:lang="fr">Russie</country>
<wicri:regionArea>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia A. P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjev ave., Novosibirsk 630090</wicri:regionArea>
</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:affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Kawaji, Hideya" sort="Kawaji, Hideya" uniqKey="Kawaji H" first="Hideya" last="Kawaji">Hideya Kawaji</name>
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<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama 351-0198</wicri:regionArea>
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<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama 351-0198</wicri:regionArea>
</affiliation>
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<author><name sortKey="Lassmann, Timo" sort="Lassmann, Timo" uniqKey="Lassmann T" first="Timo" last="Lassmann">Timo Lassmann</name>
<affiliation wicri:level="1"><nlm:affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Subiaco, 6008, Western Australia, Australia.</nlm:affiliation>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Subiaco, 6008, Western Australia</wicri:regionArea>
</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:affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045</wicri:regionArea>
</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:affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045</wicri:regionArea>
</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:affiliation>LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS</wicri:regionArea>
</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="1"><nlm:affiliation>The George Washington University Medical Center, Department of Medicine, Division of Genomic Medicine, 2300 I St. NW, Washington, DC, USA.</nlm:affiliation>
<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>
</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:affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045</wicri:regionArea>
</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:affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama 351-0198</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Wahlestedt, Claes" sort="Wahlestedt, Claes" uniqKey="Wahlestedt C" first="Claes" last="Wahlestedt">Claes Wahlestedt</name>
<affiliation wicri:level="1"><nlm:affiliation>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 clawah@gmail.com.</nlm:affiliation>
<country wicri:rule="url">Oman</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>
</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:affiliation>Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA philippk08@hotmail.com.</nlm:affiliation>
<country wicri:rule="url">Oman</country>
<wicri:regionArea>Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801</wicri:regionArea>
</affiliation>
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<series><title level="j">Nucleic acids research</title>
<idno type="eISSN">1362-4962</idno>
<imprint><date when="2016" type="published">2016</date>
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<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>
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<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>
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<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">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 vlinc RNAs genes likely function in cisto activate nearby genes. This effect while most pronounced in closely spaced vlinc RNA-gene pairs can be detected over relatively large genomic distances. Furthermore, we identified 101 vlinc RNA 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.</div>
</front>
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<DateCreated><Year>2016</Year>
<Month>04</Month>
<Day>21</Day>
</DateCreated>
<DateCompleted><Year>2016</Year>
<Month>09</Month>
<Day>21</Day>
</DateCompleted>
<DateRevised><Year>2017</Year>
<Month>02</Month>
<Day>20</Day>
</DateRevised>
<Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1362-4962</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>44</Volume>
<Issue>7</Issue>
<PubDate><Year>2016</Year>
<Month>Apr</Month>
<Day>20</Day>
</PubDate>
</JournalIssue>
<Title>Nucleic acids research</Title>
<ISOAbbreviation>Nucleic Acids Res.</ISOAbbreviation>
</Journal>
<ArticleTitle>Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.</ArticleTitle>
<Pagination><MedlinePgn>3233-52</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1093/nar/gkw162</ELocationID>
<Abstract><AbstractText>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 vlinc RNAs genes likely function in cisto activate nearby genes. This effect while most pronounced in closely spaced vlinc RNA-gene pairs can be detected over relatively large genomic distances. Furthermore, we identified 101 vlinc RNA 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.</AbstractText>
<CopyrightInformation>© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>St Laurent</LastName>
<ForeName>Georges</ForeName>
<Initials>G</Initials>
<AffiliationInfo><Affiliation>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Vyatkin</LastName>
<ForeName>Yuri</ForeName>
<Initials>Y</Initials>
<AffiliationInfo><Affiliation>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Antonets</LastName>
<ForeName>Denis</ForeName>
<Initials>D</Initials>
<AffiliationInfo><Affiliation>AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia State Research Center of Virology and Biotechnology 'Vector', Novosibirsk, Russia A. P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Ri</LastName>
<ForeName>Maxim</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Qi</LastName>
<ForeName>Yao</ForeName>
<Initials>Y</Initials>
<AffiliationInfo><Affiliation>Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Saik</LastName>
<ForeName>Olga</ForeName>
<Initials>O</Initials>
<AffiliationInfo><Affiliation>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia Federal Research Center Institute of Cytology and Genetics SB RAS, 10, Acad. Lavrentjev ave., Novosibirsk 630090, Russia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Shtokalo</LastName>
<ForeName>Dmitry</ForeName>
<Initials>D</Initials>
<AffiliationInfo><Affiliation>St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA AcademGene Ltd., 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia A. P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>de Hoon</LastName>
<ForeName>Michiel J L</ForeName>
<Initials>MJ</Initials>
<AffiliationInfo><Affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Kawaji</LastName>
<ForeName>Hideya</ForeName>
<Initials>H</Initials>
<AffiliationInfo><Affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Itoh</LastName>
<ForeName>Masayoshi</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Lassmann</LastName>
<ForeName>Timo</ForeName>
<Initials>T</Initials>
<AffiliationInfo><Affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Subiaco, 6008, Western Australia, Australia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Arner</LastName>
<ForeName>Erik</ForeName>
<Initials>E</Initials>
<AffiliationInfo><Affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Forrest</LastName>
<ForeName>Alistair R R</ForeName>
<Initials>AR</Initials>
<AffiliationInfo><Affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><CollectiveName>FANTOM consortium</CollectiveName>
</Author>
<Author ValidYN="Y"><LastName>Nicolas</LastName>
<ForeName>Estelle</ForeName>
<Initials>E</Initials>
<AffiliationInfo><Affiliation>LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>McCaffrey</LastName>
<ForeName>Timothy A</ForeName>
<Initials>TA</Initials>
<AffiliationInfo><Affiliation>The George Washington University Medical Center, Department of Medicine, Division of Genomic Medicine, 2300 I St. NW, Washington, DC, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Carninci</LastName>
<ForeName>Piero</ForeName>
<Initials>P</Initials>
<AffiliationInfo><Affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Hayashizaki</LastName>
<ForeName>Yoshihide</ForeName>
<Initials>Y</Initials>
<AffiliationInfo><Affiliation>RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Wahlestedt</LastName>
<ForeName>Claes</ForeName>
<Initials>C</Initials>
<AffiliationInfo><Affiliation>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 clawah@gmail.com.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Kapranov</LastName>
<ForeName>Philipp</ForeName>
<Initials>P</Initials>
<AffiliationInfo><Affiliation>Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA philippk08@hotmail.com.</Affiliation>
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<Language>eng</Language>
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<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
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<ArticleDate DateType="Electronic"><Year>2016</Year>
<Month>03</Month>
<Day>21</Day>
</ArticleDate>
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<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Nucleic Acids Res</MedlineTA>
<NlmUniqueID>0411011</NlmUniqueID>
<ISSNLinking>0305-1048</ISSNLinking>
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	Serveur d'exploration sur les relations entre la France et l'Australie
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Serveur d'exploration sur les relations entre la France et l'Australie

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

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