Show simple item record

dc.contributor.authorde Rie, Derek
dc.contributor.authorAbugessaisa, Imad
dc.contributor.authorAlam, Tanvir
dc.contributor.authorArner, Erik
dc.contributor.authorArner, Peter
dc.contributor.authorAshoor, Haitham
dc.contributor.authorAstrom, Gaby
dc.contributor.authorBabina, Magda
dc.contributor.authorBertin, Nicolas
dc.contributor.authorBurroughs, A. Maxwell
dc.contributor.authorCarlisle, Ailsa J.
dc.contributor.authorDaub, Carsten O.
dc.contributor.authorDetmar, Michael
dc.contributor.authorDeviatiiarov, Ruslan
dc.contributor.authorFort, Alexandre
dc.contributor.authorGebhard, Claudia
dc.contributor.authorGoldowitz, Daniel
dc.contributor.authorGuhl, Sven
dc.contributor.authorHa, Thomas J.
dc.contributor.authorHarshbarger, Jayson
dc.contributor.authorHasegawa, Akira
dc.contributor.authorHashimoto, Kosuke
dc.contributor.authorHerlyn, Meenhard
dc.contributor.authorHeutink, Peter
dc.contributor.authorHitchens, Kelly J.
dc.contributor.authorHon, Chung Chau
dc.contributor.authorHuang, Edward
dc.contributor.authorIshizu, Yuri
dc.contributor.authorKai, Chieko
dc.contributor.authorKasukawa, Takeya
dc.contributor.authorKlinken, Peter
dc.contributor.authorLassmann, Timo
dc.contributor.authorLecellier, Charles-Henri
dc.contributor.authorLee, Weonju
dc.contributor.authorLizio, Marina
dc.contributor.authorMakeev, Vsevolod
dc.contributor.authorMathelier, Anthony
dc.contributor.authorMedvedeva, Yulia A.
dc.contributor.authorMejhert, Niklas
dc.contributor.authorMungall, Christopher J.
dc.contributor.authorNoma, Shohei
dc.contributor.authorOhshima, Mitsuhiro
dc.contributor.authorOkada-Hatakeyama, Mariko
dc.contributor.authorPersson, Helena
dc.contributor.authorRizzu, Patrizia
dc.contributor.authorRoudnicky, Filip
dc.contributor.authorSaetrom, Pal
dc.contributor.authorSato, Hiroki
dc.contributor.authorSeverin, Jessica
dc.contributor.authorShin, Jay W.
dc.contributor.authorSwoboda, Rolf K.
dc.contributor.authorTarui, Hiroshi
dc.contributor.authorToyoda, Hiroo
dc.contributor.authorVitting-Seerup, Kristoffer
dc.contributor.authorWinteringham, Louise
dc.contributor.authorYamaguchi, Yoko
dc.contributor.authorYasuzawa, Kayoko
dc.contributor.authorYoneda, Misako
dc.contributor.authorYumoto, Noriko
dc.contributor.authorZabierowski, Susan
dc.contributor.authorZhang, Peter G.
dc.contributor.authorWells, Christine A.
dc.contributor.authorSummers, Kim M.
dc.contributor.authorKawaji, Hideya
dc.contributor.authorSandelin, Albin
dc.contributor.authorRehli, Michael
dc.contributor.authorHayashizaki, Yoshihide
dc.contributor.authorCarninci, Piero
dc.contributor.authorForrest, Alistair R. R.
dc.contributor.authorde Hoon, Michiel J. L.
dc.date.accessioned2021-07-08T10:26:28Z
dc.date.available2021-07-08T10:26:28Z
dc.date.issued2017
dc.identifier.citationDe Rie, D., Abugessaisa, I., Alam, T., Arner, E., Arner, P., … Bertin, N. (2017). An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature Biotechnology, 35(9), 872–878. doi:10.1038/nbt.3947
dc.identifier.issn1546-1696
dc.identifier.issn1087-0156
dc.identifier.pmid28829439
dc.identifier.doi10.1038/nbt.3947
dc.identifier.urihttp://hdl.handle.net/10754/670083
dc.description.abstractMicroRNAs (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.
dc.description.sponsorshipFANTOM5 was made possible by the following grants: Research Grant for RIKEN Omics Science Center from MEXT to Y.H.; Grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT to Y.H.; Research Grant from MEXT to the RIKEN Center for Life Science Technologies; Research Grant to RIKEN Preventive Medicine and Diagnosis Innovation Program from MEXT to Y.H. K.V.-S. and A.S. were supported by the Lundbeck and Novo Nordisk Foundations. A.R.R.F. is supported by a Senior Cancer Research Fellowship from the Cancer Research Trust, funds raised by the MACA Ride to Conquer Cancer, and the Australian Research Council’s Discovery Projects funding scheme (DP160101960). Y.A.M. was supported by the Russian Science Foundation, grant 15-14-30002. R.D. was supported by the Russian Science Foundation, grant 14-44-00022. We would like to thank L. Schwarzfischer for technical assistance and N. Eichner and G. Meister for sequencing RACE products. We would also like to thank GeNAS for data production.
dc.publisherSpringer Science and Business Media LLC
dc.relation.urlhttp://www.nature.com/articles/nbt.3947
dc.rightsArchived with thanks to NATURE BIOTECHNOLOGY
dc.titleAn integrated expression atlas of miRNAs and their promoters in human and mouse
dc.typeArticle
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.identifier.journalNATURE BIOTECHNOLOGY
dc.identifier.pmcidPMC5767576
dc.identifier.wosutWOS:000410371600022
dc.eprint.versionPost-print
dc.contributor.institutionDivision of Genomic Technologies, RIKEN, Center for Life Science Technologies, Yokohama, Japan
dc.contributor.institutionCentre for Integrative Bioinformatics, VU University Amsterdam, Amsterdam, Netherlands
dc.contributor.institutionRIKEN Omics Science Center, Yokohama, Japan
dc.contributor.institutionDepartment of Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
dc.contributor.institutionDepartment of Dermatology and Allergy, Charité Campus Mitte, Universitätsmedizin Berlin, Berlin, Germany
dc.contributor.institutionCancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
dc.contributor.institutionNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
dc.contributor.institutionRoslin Institute and Royal, School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
dc.contributor.institutionInstitute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zürich, Switzerland
dc.contributor.institutionInstitute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
dc.contributor.institutionDepartment of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
dc.contributor.institutionRegensburg Centre for Interventional Immunology, Regensburg, Germany
dc.contributor.institutionDepartment of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
dc.contributor.institutionMelanoma Research Center, Wistar Institute, Philadelphia, PA, United States
dc.contributor.institutionGerman Center for Neurodegenerative Diseases, Tübingen, Germany
dc.contributor.institutionAustralian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
dc.contributor.institutionUniversity of Melbourne Centre for Stem Cell Systems, School of Biomedical Sciences, University of Melbourne, Melbourne, VIC, Australia
dc.contributor.institutionWalter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
dc.contributor.institutionLaboratory Animal Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
dc.contributor.institutionHarry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, QEII Medical Centre, Perth, WA, Australia
dc.contributor.institutionTelethon Kids Institute, University of Western Australia, Subiaco, WA, Australia
dc.contributor.institutionInstitute of Molecular Genetics of Montpellier, Montpellier, France
dc.contributor.institutionDepartment of Dermatology, Kyungpook National University, School of Medicine, Daegu, South Korea
dc.contributor.institutionVavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russian Federation
dc.contributor.institutionEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
dc.contributor.institutionMoscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
dc.contributor.institutionIMPPC, Institute of Predictive and Personalized Medicine of Cancer, Badalona, Spain
dc.contributor.institutionInstitute of Bioengineering, Research Center of Biotechnology, Moscow, Russian Federation
dc.contributor.institutionEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
dc.contributor.institutionDepartment of Biochemistry, Ohu University, School of Pharmaceutical Sciences, Koriyama, Japan
dc.contributor.institutionLaboratory of Cell Systems, Institute for Protein Research, Osaka University, Osaka, Japan
dc.contributor.institutionRIKEN, Center for Integrative Medical Sciences, Yokohama, Japan
dc.contributor.institutionDivision of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
dc.contributor.institutionDepartment of Computer and Information Science, Norwegian University of Science and Technology, Trondheim, Norway
dc.contributor.institutionDepartment of Clinical Molecular Genetics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
dc.contributor.institutionBioinformatics Centre, Department of Biology, Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
dc.contributor.institutionDepartment of Biochemistry, Nihon University, School of Dentistry, Tokyo, Japan
dc.contributor.institutionSKI Stem Cell Research Facility, Center for Stem Cell Biology and Developmental Biology Program, Sloan Kettering Institute, New York, NY, United States
dc.contributor.institutionMater Research Institute, University of Queensland, Translational Research Institute, Brisbane, Australia
dc.contributor.institutionRIKEN, Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
dc.identifier.volume35
dc.identifier.issue9
dc.identifier.pages872-+
kaust.personAlam, Tanvir
kaust.personAshoor, Haitham
dc.identifier.eid2-s2.0-85028474852


This item appears in the following Collection(s)

Show simple item record