ArticleNature biotechnology2017
An integrated expression atlas of miRNAs and their promoters in human and mouse.
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Article in Nature biotechnology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 317 papers, 1 of them a synthesis that pooled it.
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317citing papers in PubMed, 1 pooled it
19.4field-weighted citation impact, top 1% of its field
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Who cites it
317 citing papers in PubMed, 1 synthesis or guideline pooled it, 597 citations in OpenAlex.
- The Role of microRNAs in Pulp Inflammation.Cells · 2021Pooled it
- MicroRNAs in veterinary viral diseases: A comprehensive review from molecular mechanisms to clinical translation.Virus research · 2026Review
- Intra-articular delivery of VEGF targeting miR-126-3p and miR-140-5p ameliorates synovitis and pain in a rat model of post-traumatic knee osteoarthritis.Journal of orthopaedic translation · 2026Article
- Blood-derived microRNA signatures associated with hippocampal structure and atrophy rate: findings from the Rhineland Study.Molecular psychiatry · 2026Article
- Genome-Wide CRISPR Screen Identifies a microRNA Orchestrating Pleiotropic Resistance to Targeted Therapy and T Cell Immunity in Melanoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- miRSiC: a regulatory-aware machine learning framework for microRNA expression inference across bulk and single-cell transcriptomes.Briefings in bioinformatics · 2026Article
- The Distribution of Average Pairwise Distances Among Human Pre-miRNAs for Disease Association Analysis.International journal of molecular sciences · 2026Article
- FOXO1 in cancer: context-dependent roles, microRNA regulation, and therapeutic opportunities.Discover oncology · 2026Review
- Upregulation of an Epithelial miRNA Is Associated with Immune Evasion in Progressive Bronchial Premalignant Lesions.Cancer immunology research · 2026Article
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- Enhanced muscle uptake of chemically optimized miR-23b antisense oligonucleotides as lead compounds for myotonic dystrophy type 1.American journal of human genetics · 2026Article
- High-Throughput In Vivo Screening Using Barcoded mRNA Identifies Lipid Nanoparticles With Extrahepatic Tropism for In Situ Immunoengineering.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- MicroRNAs as novel therapeutic targets against inflammatory bowel disease through modulation of ferroptosis.Clinical and experimental medicine · 2026Review
- The Role of microRNAs as Potential Biomarkers in Diffuse Large B-Cell Lymphoma.Non-coding RNA · 2026Review
- Nutriepigenetics and nutriepigenomics: Exploring the interactions between nutrition, epigenetics, and epigenomics in the pathogenesis of noncommunicable diseases.Genetics and molecular biology · 2026Article
- MicroRNAs in Asthma: A Replication-Based Review of Human Evidence.Journal of inflammation research · 2026Review
- Challenges and Perspectives in ncRNA Research.Experientia supplementum (2012) · 2026Review
- Long-read transcriptomics of a diverse human cohort reveals ancestry bias in gene annotation.Nature communications · 2025Article
- Crosstalk between miRNAs and oxidative stress: implications for cancer pathogenesis and therapy.Functional & integrative genomics · 2025Review
- MicroRNAs in neurodegenerative diseases: from molecular mechanisms to clinical biomarkers, detection methods and therapeutic strategies-advances and challenges.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2025Review
257 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
71 authors at 20 institutions in 16 countries.
Derek de RieDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Imad AbugessaisaDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.ORCID http://orcid.org/0000-0001-7458-801X
Tanvir AlamComputational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
Erik ArnerDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Peter ArnerDepartment of Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden.
Haitham AshoorComputational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
Gaby ÅströmDepartment of Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden.
Magda BabinaDepartment of Dermatology and Allergy, Charité Campus Mitte, Universitätsmedizin Berlin, Berlin, Germany.
Nicolas BertinDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.ORCID http://orcid.org/0000-0002-9835-9606
A Maxwell BurroughsDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Ailsa J CarlisleThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
Carsten O DaubDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.ORCID http://orcid.org/0000-0002-3295-8729
Michael DetmarInstitute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.ORCID http://orcid.org/0000-0002-5351-5054
Ruslan DeviatiiarovDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Alexandre FortDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Claudia GebhardDepartment of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
Daniel GoldowitzDepartment of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.
Sven GuhlDepartment of Dermatology and Allergy, Charité Campus Mitte, Universitätsmedizin Berlin, Berlin, Germany.
Thomas J HaDepartment of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.
Jayson HarshbargerDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.ORCID http://orcid.org/0000-0002-5188-2045
Akira HasegawaDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Kosuke HashimotoDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Meenhard HerlynMelanoma Research Center, The Wistar Institute, Philadelphia, Pennsylvania, USA.
Peter HeutinkGerman Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.ORCID http://orcid.org/0000-0001-5218-1737
Kelly J HitchensAustralian Infectious Diseases Research Centre (AID), University of Queensland, Brisbane, Queensland, Australia.
Chung Chau HonDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.ORCID http://orcid.org/0000-0002-3741-7577
Edward HuangThe University of Melbourne Centre for Stem Cell Systems, School of Biomedical Sciences, The University of Melbourne, Victoria, Australia.
Yuri IshizuDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Chieko KaiLaboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Takeya KasukawaDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Peter KlinkenHarry Perkins Institute of Medical Research, and the Centre for Medical Research, University of Western Australia, QEII Medical Centre, Perth, Western Australia, Australia.
Timo LassmannDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Charles-Henri LecellierDepartment of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.
Weonju LeeDepartment of Dermatology, Kyungpook National University School of Medicine, Daegu, South Korea.
Marina LizioDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.ORCID http://orcid.org/0000-0001-7337-7325
Vsevolod MakeevVavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.ORCID http://orcid.org/0000-0001-9405-9748
Anthony MathelierDepartment of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.ORCID http://orcid.org/0000-0001-5127-5459
Yulia A MedvedevaVavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
Niklas MejhertDepartment of Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden.
Christopher J MungallEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Shohei NomaDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Mitsuhiro OhshimaDepartment of Biochemistry, Ohu University School of Pharmaceutical Sciences, Koriyama, Japan.
Mariko Okada-HatakeyamaLaboratory of Cell Systems, Institute for Protein Research, Osaka University, Osaka, Japan.
Helena PerssonDivision of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden.ORCID http://orcid.org/0000-0002-5187-6446
Patrizia RizzuGerman Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
Filip RoudnickyInstitute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.ORCID http://orcid.org/0000-0001-7156-2383
Pål SætromDepartment of Computer and Information Science, Norwegian University of Science and Technology, Trondheim, Norway.ORCID http://orcid.org/0000-0001-8142-7441
Hiroki SatoLaboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Jessica SeverinDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Jay W ShinDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Rolf K SwobodaMelanoma Research Center, The Wistar Institute, Philadelphia, Pennsylvania, USA.
Hiroshi TaruiDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Hiroo ToyodaDepartment of Clinical Molecular Genetics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan.
Kristoffer Vitting-SeerupThe Bioinformatics Centre, Department of Biology, and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
Louise WinteringhamHarry Perkins Institute of Medical Research, and the Centre for Medical Research, University of Western Australia, QEII Medical Centre, Perth, Western Australia, Australia.
Yoko YamaguchiDepartment of Biochemistry, Nihon University School of Dentistry, Tokyo, Japan.
Kayoko YasuzawaDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Misako YonedaLaboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Noriko YumotoRIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
Susan ZabierowskiThe SKI Stem Cell Research Facility, The Center for Stem Cell Biology and Developmental Biology Program, Sloan Kettering Institute, New York, New York, USA.
Peter G ZhangDepartment of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.
Christine A WellsThe University of Melbourne Centre for Stem Cell Systems, School of Biomedical Sciences, The University of Melbourne, Victoria, Australia.ORCID http://orcid.org/0000-0003-3133-3628
Kim M SummersThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
Hideya KawajiDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Albin SandelinThe Bioinformatics Centre, Department of Biology, and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-7109-7378
Michael RehliDepartment of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
FANTOM Consortium
Yoshihide HayashizakiRIKEN Omics Science Center (OSC), Yokohama, Japan.
Piero CarninciDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.ORCID http://orcid.org/0000-0001-7202-7243
Alistair R R ForrestDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Michiel J L de HoonDivision of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
RIKEN Center for Integrative Medical Sciences · JPUniversity of British Columbia · CAKarolinska University Hospital · SEThe University of Tokyo · JPThe University of Western Australia · AUCharité - Universitätsmedizin Berlin · DEETH Zurich · CHGerman Center for Neurodegenerative Diseases · DEKing Abdullah University of Science and Technology · SARIKEN · JPThe University of Melbourne · AUThe Wistar Institute · USUniversity Hospital Regensburg · DEUniversity of Copenhagen · DKBioengineering Center · RUEngelhardt Institute of Molecular Biology · RUKazan Federal University · RUKettering University · USKyungpook National University · KRLawrence Berkeley National Laboratory · US
Funding
Tumor Microenvironment and MetastasisP30CA010815 · NCI · WISTAR INSTITUTE · PI Luis J Montaner · 1985 to 2026
$75.9MBiotechnology and Biological Sciences Research Council BB/I024801/1Biotechnology and Biological Sciences Research Council BBS/E/D/20211550Biotechnology and Biological Sciences Research Council BBS/E/D/20211551Biotechnology and Biological Sciences Research Council BBS/E/D/20211552NCI NIH HHS P30 CA010815
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.
Indexed as
Molecular Sequence AnnotationAnimalsCells, CulturedGene Expression ProfilingGene LibraryHigh-Throughput Nucleotide SequencingHumansMiceMicroRNAsPromoter Regions, GeneticMicroRNAs
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