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Nat Biotechnol. 2017 Sep;35(9):872-878. doi: 10.1038/nbt.3947. Epub 2017 Aug 21.

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

Author information

1
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
2
Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam, the Netherlands.
3
Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
4
RIKEN Omics Science Center (OSC), Yokohama, Japan.
5
Department of Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden.
6
Department of Dermatology and Allergy, Charité Campus Mitte, Universitätsmedizin Berlin, Berlin, Germany.
7
Cancer Science Institute of Singapore, National University of Singapore, Singapore.
8
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
9
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
10
Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.
11
Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia.
12
Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
13
Regensburg Centre for Interventional Immunology (RCI), Regensburg, Germany.
14
Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.
15
Melanoma Research Center, The Wistar Institute, Philadelphia, Pennsylvania, USA.
16
German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
17
Australian Infectious Diseases Research Centre (AID), University of Queensland, Brisbane, Queensland, Australia.
18
The University of Melbourne Centre for Stem Cell Systems, School of Biomedical Sciences, The University of Melbourne, Victoria, Australia.
19
Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
20
Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
21
Harry Perkins Institute of Medical Research, and the Centre for Medical Research, University of Western Australia, QEII Medical Centre, Perth, Western Australia, Australia.
22
Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia, Australia.
23
Institute of Molecular Genetics of Montpellier, Montpellier, France.
24
Department of Dermatology, Kyungpook National University School of Medicine, Daegu, South Korea.
25
Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
26
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
27
Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
28
IMPPC, Institute of Predictive and Personalized Medicine of Cancer, Ctra. de Can Ruti, Badalona, Spain.
29
Institute of Bioengineering, Research Center of Biotechnology, Moscow, Russia.
30
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
31
Department of Biochemistry, Ohu University School of Pharmaceutical Sciences, Koriyama, Japan.
32
Laboratory of Cell Systems, Institute for Protein Research, Osaka University, Osaka, Japan.
33
RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
34
Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden.
35
Department of Computer and Information Science, Norwegian University of Science and Technology, Trondheim, Norway.
36
Department of Clinical Molecular Genetics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan.
37
The Bioinformatics Centre, Department of Biology, and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
38
Department of Biochemistry, Nihon University School of Dentistry, Tokyo, Japan.
39
The SKI Stem Cell Research Facility, The Center for Stem Cell Biology and Developmental Biology Program, Sloan Kettering Institute, New York, New York, USA.
40
Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Australia.
41
RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan.

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.

PMID:
28829439
PMCID:
PMC5767576
DOI:
10.1038/nbt.3947
[Indexed for MEDLINE]
Free PMC Article

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