An integrated expression atlas of miRNAs and their promoters in human and mouse

Research output: Contribution to journalArticle


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.


  • Derek De Rie
  • Imad Abugessaisa
  • Tanvir Alam
  • Erik Arner
  • Peter Arner
  • Haitham Ashoor
  • Gaby Åström
  • Magda Babina
  • Nicolas Bertin
  • A. Maxwell Burroughs
  • Ailsa J. Carlisle
  • Carsten O. Daub
  • Michael Detmar
  • Ruslan Deviatiiarov
  • Alexandre Fort
  • Claudia Gebhard
  • Daniel Goldowitz
  • Sven Guhl
  • Thomas J. Ha
  • Jayson Harshbarger
  • Akira Hasegawa
  • Kosuke Hashimoto
  • Meenhard Herlyn
  • Peter Heutink
  • Kelly J. Hitchens
  • Chung Chau Hon
  • Edward Huang
  • Yuri Ishizu
  • Chieko Kai
  • Takeya Kasukawa
  • Peter Klinken
  • Timo Lassmann
  • Charles Henri Lecellier
  • Weonju Lee
  • Marina Lizio
  • Vsevolod Makeev
  • Anthony Mathelier
  • Yulia A. Medvedeva
  • Niklas Mejhert
  • Christopher J. Mungall
  • Shohei Noma
  • Mitsuhiro Ohshima
  • Mariko Okada-Hatakeyama
  • Patrizia Rizzu
  • Filip Roudnicky
  • Pål Sætrom
  • Hiroki Sato
  • Jessica Severin
  • Jay W. Shin
  • Rolf K. Swoboda
  • Hiroshi Tarui
  • Hiroo Toyoda
  • Kristoffer Vitting-Seerup
  • Louise Winteringham
  • Yoko Yamaguchi
  • Kayoko Yasuzawa
  • Misako Yoneda
  • Noriko Yumoto
  • Susan Zabierowski
  • Peter G. Zhang
  • Christine A. Wells
  • Kim M. Summers
  • Hideya Kawaji
  • Albin Sandelin
  • Michael Rehli
  • Yoshihide Hayashizaki
  • Piero Carninci
  • Alistair R.R. Forrest
  • Michiel J.L. De Hoon
External organisations
  • Karolinska University Hospital
  • Charité Universitätsmedizin Berlin
  • University of Edinburgh
  • ETH Zürich
  • Kazan Federal University
  • University Hospital Regensburg
  • University of Regensburg
  • University of British Columbia
  • The Wistar Institute
  • German Center for Neurodegenerative Diseases (DZNE), Bonn
  • University of Queensland
  • University of Melbourne
  • Walter and Eliza Hall Institute of Medical Research
  • University of Western Australia, Crawley
  • Institut de Génétique Moléculaire de Montpellier
  • Kyungpook National University
  • Institute of Applied Physics, RAS
  • Engelhardt Institute of Molecular Biology, RAS
  • Moscow Institute of Physics and Technology
  • Institute of Predictive and Personalized Medicine of Cancer
  • Institute of Bioengineering, RAS
  • Lawrence Berkeley National Laboratory
  • Ohu University
  • Osaka University
  • Norwegian University of Science and Technology
  • Tokyo University of Pharmacy and Life Sciences
  • University of Copenhagen
  • Nihon University
  • RIKEN Center for Life Science Technologies
  • Vrije Universiteit Amsterdam
  • King Abdullah University of Science and Technology
  • RIKEN Omics Science Center
  • Karolinska Institutet
  • National University of Singapore
  • National Library of Medicine; USA
  • University of Tokyo
  • RIKEN Center for Integrative Medical Sciences
  • Memorial Sloan-Kettering Cancer Center
  • RIKEN Preventive Medicine and Diagnosis Innovation Program
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Cell Biology
  • Cell and Molecular Biology
Original languageEnglish
Pages (from-to)872-878
Number of pages7
JournalNature Biotechnology
Issue number9
Publication statusPublished - 2017 Sep 1
Publication categoryResearch