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

Yoko de Rie; Yoko Abugessaisa; Tanvir Alam; Yoko Arner; Peter Arner; Haitham Ha; Gaby Aström; Magda Babina; 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; Kelly Hitchens; Yoko Hon; Edward Huang; Yoko Ishizu; Chieko Kai; Yoko Kasukawa; Peter Klinken; Yoko Lassmann; Charles-Henri Lecellier; Weonju Lee; Yoko Lizio; Vsevolod Makeev; Anthony Mathelier; Yulia Medvedeva; Niklas Mejhert; Christopher Mungall; Yoko Noma; Mitsuhiro Ohshima; Yoko Okada-Hatakeyama; Helena Persson; Patrizia Rizzu; 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; Albin Sandelin; Michael Rehli; Yoshihide Hayashizaki; Piero Carninci; Alistair Forrest; Michiel J.L. de Hoon; Derek de Rie; Imad Abugessaisa; Erik Arner; Haitham Ashoor; Nicolas Bertin; a Maxwell Burroughs; Carsten Daub; Ruslan Deviatiiarov; Alexandre Fort; Jayson Ha; Akira Ha; Kosuke Ha; Chung Chau Hon; Yuri Ishizu; Takeya Kasukawa; Timo Lassmann; Marina Lizio; Shohei Noma; Mariko Ha; Jessica Severin; Jay Shin; Hiroshi Tarui; Yoshihide Ha

doi:10.1038/nbt.3947

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

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

Yoko de Rie, Yoko Abugessaisa, Tanvir Alam, Yoko Arner, Peter Arner, Haitham Ha, Gaby Aström, Magda Babina, Yoko Bertin, Yoko Burroughs, …

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

21/08/2017

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

PMCID: PMC5767576

PMID: 28829439

Résumé

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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Titre: An integrated expression atlas of miRNAs and their promoters in human and mouse
Créateurs - sans rôle: Yoko de Rie
Yoko Abugessaisa
Tanvir Alam - King Abdullah University of Science and Technology
Yoko Arner
Peter Arner - Karolinska University Hospital
Haitham Ha
Gaby Aström - Karolinska University Hospital
Magda Babina - Charité - Universitätsmedizin Berlin
Yoko Bertin
Yoko Burroughs
Ailsa Carlisle - Roslin Institute
Yoko Daub
Michael Detmar - ETH Zurich
Yoko Deviatiiarov
Yoko Fort
Claudia Gebhard - University Hospital Regensburg
Daniel Goldowitz
Sven Guhl - Charité - Universitätsmedizin Berlin
Thomas Ha - University of British Columbia
Yoko Harshbarger
Yoko Hasegawa
Yoko Hashimoto
Meenhard Herlyn - The Wistar Institute
Peter Heutink - German Center for Neurodegenerative Diseases
Kelly Hitchens - The University of Queensland
Yoko Hon
Edward Huang - The University of Melbourne
Yoko Ishizu
Chieko Kai - The University of Tokyo
Yoko Kasukawa
Peter Klinken - Harry Perkins Institute of Medical Research
Yoko Lassmann
Charles-Henri Lecellier - Université de Montpellier, Institut de Génétique Moléculaire de Montpellier - IGMM
Weonju Lee
Yoko Lizio
Vsevolod Makeev - Vavilov Institute of General Genetics
Anthony Mathelier - University of British Columbia
Yulia Medvedeva - Vavilov Institute of General Genetics
Niklas Mejhert - Karolinska University Hospital
Christopher Mungall
Yoko Noma
Mitsuhiro Ohshima - Ohu University
Yoko Okada-Hatakeyama
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
Yoko Severin
Yoko Shin
Rolf Swoboda - The Wistar Institute
Yoko Tarui
Hiroo Toyoda - Tokyo University of Pharmacy and Life Sciences
Kristoffer Vitting-Seerup - University of Copenhagen
Louise Winteringham - The University of Western Australia
Yoko Yamaguchi - Nihon University
Kayoko Yasuzawa
Misako Yoneda - The University of Tokyo
Noriko Yumoto - RIKEN Center for Integrative Medical Sciences
Susan Zabierowski - Kettering University
Peter Zhang - University of British Columbia
Christine Wells - The University of Melbourne
Kim Summers - The University of Queensland
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 Forrest
Michiel J.L. de Hoon
Derek de Rie
Imad Abugessaisa - Ctr Life Sci Technol, Div Gen Technol, Tsurumi Ku
Erik Arner - Karolinska Institutet
Haitham Ashoor - King Abdullah University of Science and Technology
Nicolas Bertin - RIKEN Center for Integrative Medical Sciences
a Maxwell Burroughs - RIKEN Center for Integrative Medical Sciences
Carsten Daub - RIKEN Center for Integrative Medical Sciences
Ruslan Deviatiiarov
Alexandre Fort - RIKEN Center for Integrative Medical Sciences
Jayson Ha
Akira Ha
Kosuke Ha
Chung Chau Hon
Yuri Ishizu - RIKEN Center for Integrative Medical Sciences
Takeya Kasukawa - Ctr Life Sci Technol, Div Gen Technol, Tsurumi Ku
Timo Lassmann - RIKEN Center for Integrative Medical Sciences
Marina Lizio - RIKEN Center for Integrative Medical Sciences
Shohei Noma - RIKEN Center for Integrative Medical Sciences
Mariko Ha
Jessica Severin - RIKEN Center for Integrative Medical Sciences
Jay Shin - RIKEN Center for Integrative Medical Sciences
Hiroshi Tarui - RIKEN Center for Integrative Medical Sciences
Yoshihide Ha
Détails de publication: Nature Biotechnology, Vol.35(9), pp.872-878
Identifiants: 99153564209311
Unité académique: Institut de Génétique Moléculaire de Montpellier - IGMM
Langue: English
Type de ressource: Journal article
Champs locaux: hal-02106433