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An integrated expression atlas of miRNAs and their promoters in human and mouse.
de Rie, Derek; Abugessaisa, Imad; Alam, Tanvir; Arner, Erik; Arner, Peter; Ashoor, Haitham; Åström, Gaby; Babina, Magda; Bertin, Nicolas; Burroughs, A Maxwell; Carlisle, Ailsa J; Daub, Carsten O; Detmar, Michael; Deviatiiarov, Ruslan; Fort, Alexandre; Gebhard, Claudia; Goldowitz, Daniel; Guhl, Sven; Ha, Thomas J; Harshbarger, Jayson; Hasegawa, Akira; Hashimoto, Kosuke; Herlyn, Meenhard; Heutink, Peter; Hitchens, Kelly J; Hon, Chung Chau; Huang, Edward; Ishizu, Yuri; Kai, Chieko; Kasukawa, Takeya; Klinken, Peter; Lassmann, Timo; Lecellier, Charles-Henri; Lee, Weonju; Lizio, Marina; Makeev, Vsevolod; Mathelier, Anthony; Medvedeva, Yulia A; Mejhert, Niklas; Mungall, Christopher J; Noma, Shohei; Ohshima, Mitsuhiro; Okada-Hatakeyama, Mariko; Persson, Helena; Rizzu, Patrizia; Roudnicky, Filip; Sætrom, Pål; Sato, Hiroki; Severin, Jessica; Shin, Jay W.
Afiliação
  • de Rie D; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Abugessaisa I; Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam, the Netherlands.
  • Alam T; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Arner E; Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
  • Arner P; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Ashoor H; RIKEN Omics Science Center (OSC), Yokohama, Japan.
  • Åström G; Department of Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden.
  • Babina M; Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
  • Bertin N; Department of Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden.
  • Burroughs AM; Department of Dermatology and Allergy, Charité Campus Mitte, Universitätsmedizin Berlin, Berlin, Germany.
  • Carlisle AJ; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Daub CO; RIKEN Omics Science Center (OSC), Yokohama, Japan.
  • Detmar M; Cancer Science Institute of Singapore, National University of Singapore, Singapore.
  • Deviatiiarov R; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Fort A; RIKEN Omics Science Center (OSC), Yokohama, Japan.
  • Gebhard C; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
  • Goldowitz D; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
  • Guhl S; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Ha TJ; RIKEN Omics Science Center (OSC), Yokohama, Japan.
  • Harshbarger J; Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.
  • Hasegawa A; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Hashimoto K; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia.
  • Herlyn M; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Heutink P; RIKEN Omics Science Center (OSC), Yokohama, Japan.
  • Hitchens KJ; Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
  • Hon CC; Regensburg Centre for Interventional Immunology (RCI), Regensburg, Germany.
  • Huang E; Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.
  • Ishizu Y; Department of Dermatology and Allergy, Charité Campus Mitte, Universitätsmedizin Berlin, Berlin, Germany.
  • Kai C; Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.
  • Kasukawa T; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Klinken P; RIKEN Omics Science Center (OSC), Yokohama, Japan.
  • Lassmann T; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Lecellier CH; RIKEN Omics Science Center (OSC), Yokohama, Japan.
  • Lee W; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Lizio M; RIKEN Omics Science Center (OSC), Yokohama, Japan.
  • Makeev V; Melanoma Research Center, The Wistar Institute, Philadelphia, Pennsylvania, USA.
  • Mathelier A; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
  • Medvedeva YA; Australian Infectious Diseases Research Centre (AID), University of Queensland, Brisbane, Queensland, Australia.
  • Mejhert N; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Mungall CJ; The University of Melbourne Centre for Stem Cell Systems, School of Biomedical Sciences, The University of Melbourne, Victoria, Australia.
  • Noma S; Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
  • Ohshima M; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Okada-Hatakeyama M; RIKEN Omics Science Center (OSC), Yokohama, Japan.
  • Persson H; Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
  • Rizzu P; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Roudnicky F; Harry Perkins Institute of Medical Research, and the Centre for Medical Research, University of Western Australia, QEII Medical Centre, Perth, Western Australia, Australia.
  • Sætrom P; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
  • Sato H; RIKEN Omics Science Center (OSC), Yokohama, Japan.
  • Severin J; Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia, Australia.
  • Shin JW; Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.
Nat Biotechnol ; 35(9): 872-878, 2017 Sep.
Article em En | MEDLINE | ID: mdl-28829439
ABSTRACT
MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Regiões Promotoras Genéticas / Perfilação da Expressão Gênica / MicroRNAs / Anotação de Sequência Molecular Limite: Animals / Humans Idioma: En Ano de publicação: 2017 Tipo de documento: Article
Texto completo
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XML
PubMed Links
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Regiões Promotoras Genéticas / Perfilação da Expressão Gênica / MicroRNAs / Anotação de Sequência Molecular Limite: Animals / Humans Idioma: En Ano de publicação: 2017 Tipo de documento: Article