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

Yoko de Rie , Yoko Abugessaisa , Tanvir Alam (1) , Yoko Arner , Peter Arner (2) , Haitham Ha , Gaby Aström (2) , Magda Babina (3) , Yoko Bertin , Yoko Burroughs , Ailsa Carlisle , Yoko Daub , Michael Detmar , Yoko Deviatiiarov , Yoko Fort , Claudia Gebhard , Daniel Goldowitz , Sven Guhl , Thomas Ha , Yoko Harshbarger , Yoko Hasegawa , Yoko Hashimoto , Meenhard Herlyn , Peter Heutink (4) , Kelly Hitchens , Yoko Hon , Edward Huang , Yoko Ishizu , Chieko Kai , Yoko Kasukawa , Peter Klinken , Yoko Lassmann , Charles-Henri Lecellier (5) , Weonju Lee , Yoko Lizio , Vsevolod Makeev (6) , Anthony Mathelier (7) , Yulia Medvedeva , Niklas Mejhert (2) , Christopher Mungall , Yoko Noma , Mitsuhiro Ohshima , Yoko Okada-Hatakeyama , Helena Persson (8) , Patrizia Rizzu (4) , Filip Roudnicky , Pål Sætrom , Hiroki Sato , Yoko Severin , Yoko Shin , Rolf Swoboda , Yoko Tarui , Hiroo Toyoda , Kristoffer Vitting-Seerup , Louise Winteringham , Yoko Yamaguchi , Kayoko Yasuzawa , Misako Yoneda , Noriko Yumoto , Susan Zabierowski , Peter Zhang , Christine Wells , Kim Summers , Hideya Kawaji (9) , Albin Sandelin (10) , Michael Rehli , Yoshihide Hayashizaki (11) , Piero Carninci (12) , Alistair Forrest , Michiel J.L. de Hoon , Derek de Rie , Imad Abugessaisa (13) , Erik Arner (14) , Haitham Ashoor , Nicolas Bertin (12) , a Maxwell Burroughs , Carsten Daub , Ruslan Deviatiiarov , Alexandre Fort (15) , Jayson Ha , Akira Ha , Kosuke Ha , Chung Chau Hon , Yuri Ishizu , Takeya Kasukawa (13) , Timo Lassmann (16) , Marina Lizio (13) , Shohei Noma (13) , Mariko Ha , Jessica Severin (13) , Jay Shin , Hiroshi Tarui , Yoshihide Ha

1 Computat Biosci Res Ctr, Comp Elect & Math Sci & Engn Div
2 Department of medicine [Stockholm]
3 Dept Dermatol & Allergy
4 Department of Clinical Genetics
5 IGMM - Institut de Génétique Moléculaire de Montpellier
6 Institute of Genetics and Selection of Industrial Microorganisms
7 NCMM - Centre for Molecular Medicine Norway
8 Department of Oncology
9 RIKEN - RIKEN - Institute of Physical and Chemical Research [Japon]
10 UCPH - University of Copenhagen = Københavns Universitet
11 Cold Spring Harbor Laboratory
12 RIKEN CLST - RIKEN Center for Life Science Technologies
13 Ctr Life Sci Technol, Div Gen Technol, Tsurumi Ku
14 Karolinska Institutet [Stockholm]
15 Department of Genetic Medicine and Development [Geneva]
16 Riken Omics Science Center

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.

Domaines: Génomique, Transcriptomique et Protéomique [q-bio.GN]

Yoko de Rie, Yoko Abugessaisa, Tanvir Alam, Yoko Arner, Peter Arner, et al.. An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature Biotechnology, 2017, 35 (9), pp.872-878. ⟨10.1038/nbt.3947⟩. ⟨hal-02106433⟩