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

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; Helena Persson; 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; FANTOM Consortium

doi:10.1038/nbt.3947

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

Journal article

Peer reviewed

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

Derek de Rie, Imad Abugessaisa, Tanvir Alam, Erik Arner, Peter Arner, Haitham Ashoor, Gaby Åström, Magda Babina, Nicolas Bertin, A Maxwell Burroughs, …

Nature biotechnology, Vol.35(9), pp.872-878

01/09/2017

DOI: https://doi.org/10.1038/nbt.3947

PMCID: PMC5767576

PMID: 28829439

Abstract

Animals

Cells, Cultured

Gene Expression Profiling - methods

Gene Library

High-Throughput Nucleotide Sequencing

Humans

Mice

MicroRNAs - genetics

MicroRNAs - metabolism

Molecular Sequence Annotation

Promoter Regions, Genetic - genetics

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.

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Title: An integrated expression atlas of miRNAs and their promoters in human and mouse
Creators - without role: Derek de Rie - University of Amsterdam
Imad Abugessaisa - Genomic
Tanvir Alam - King Abdullah University of Science and Technology
Erik Arner - RIKEN
Peter Arner - Karolinska Institutet
Haitham Ashoor - King Abdullah University of Science and Technology
Gaby Åström - Karolinska University Hospital
Magda Babina - Charité - Universitätsmedizin Berlin
Nicolas Bertin - RIKEN Center for Integrative Medical Sciences
A Maxwell Burroughs - RIKEN Center for Integrative Medical Sciences
Ailsa J Carlisle - Roslin Institute
Carsten O Daub - RIKEN Center for Integrative Medical Sciences
Michael Detmar - ETH Zurich
Ruslan Deviatiiarov - Kazan Federal University
Alexandre Fort - RIKEN Center for Integrative Medical Sciences
Claudia Gebhard - University Hospital Regensburg
Daniel Goldowitz - University of British Columbia
Sven Guhl - Charité - Universitätsmedizin Berlin
Thomas J Ha - University of British Columbia
Jayson Harshbarger - RIKEN Center for Integrative Medical Sciences
Akira Hasegawa - RIKEN Center for Integrative Medical Sciences
Kosuke Hashimoto - RIKEN Center for Integrative Medical Sciences
Meenhard Herlyn - The Wistar Institute
Peter Heutink - German Center for Neurodegenerative Diseases
Kelly J Hitchens - University of Queensland
Chung Chau Hon - Genomic
Edward Huang - University of Melbourne
Yuri Ishizu - RIKEN Center for Integrative Medical Sciences
Chieko Kai - The University of Tokyo
Takeya Kasukawa - Genomic
Peter Klinken - Harry Perkins Institute of Medical Research
Timo Lassmann - RIKEN Center for Integrative Medical Sciences
Charles-Henri Lecellier - Institut de Génétique Moléculaire de Montpellier
Weonju Lee - Kyungpook National University
Marina Lizio - RIKEN Center for Integrative Medical Sciences
Vsevolod Makeev - Vavilov Institute of General Genetics
Anthony Mathelier - University of British Columbia
Yulia A Medvedeva - Vavilov Institute of General Genetics
Niklas Mejhert - Karolinska Institutet
Christopher J Mungall - Lawrence Berkeley National Laboratory
Shohei Noma - RIKEN Center for Integrative Medical Sciences
Mitsuhiro Ohshima - Ohu University
Mariko Okada-Hatakeyama - Protein Research Foundation
Helena Persson - Lund University
Patrizia Rizzu - German Center for Neurodegenerative Diseases
Filip Roudnicky - ETH Zurich
Pål Sætrom - Norwegian University of Science and Technology
Hiroki Sato - The University of Tokyo
Jessica Severin - RIKEN Center for Integrative Medical Sciences
Jay W Shin - RIKEN Center for Integrative Medical Sciences
Rolf K Swoboda - The Wistar Institute
Hiroshi Tarui - RIKEN Center for Integrative Medical Sciences
Hiroo Toyoda - Tokyo University of Pharmacy and Life Sciences
Kristoffer Vitting-Seerup - University of Copenhagen
Louise Winteringham - University of Western Australia
Yoko Yamaguchi - Nihon University
Kayoko Yasuzawa - Genomic
Misako Yoneda - The University of Tokyo
Noriko Yumoto - RIKEN Center for Integrative Medical Sciences
Susan Zabierowski - Kettering University
Peter G Zhang - University of British Columbia
Christine A Wells - University of Melbourne
Kim M Summers - University of Edinburgh
Hideya Kawaji - RIKEN
Albin Sandelin - University of Copenhagen
Michael Rehli - University Hospital Regensburg
Yoshihide Hayashizaki - RIKEN
Piero Carninci - RIKEN Center for Integrative Medical Sciences
Alistair R R Forrest - RIKEN Center for Integrative Medical Sciences
Michiel J L de Hoon - RIKEN Center for Integrative Medical Sciences
FANTOM Consortium
Publication Details: Nature biotechnology, Vol.35(9), pp.872-878
Grant note: BBS/E/D/20211551 / Biotechnology and Biological Sciences Research Council BB/I024801/1 / Biotechnology and Biological Sciences Research Council BBS/E/D/20211552 / Biotechnology and Biological Sciences Research Council P30 CA010815 / NCI NIH HHS BBS/E/D/20211550 / Biotechnology and Biological Sciences Research Council
Identifiers: 9941911408331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article