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

The FANTOM Consortium; Derek de Rie

doi:10.1038/nbt.3947

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

The FANTOM Consortium, Derek de Rie

Royal (Dick) School of Veterinary Studies

Research output: Contribution to journal › Article › peer-review

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

Original language	English
Pages (from-to)	872-878
Journal	Nature Biotechnology
Volume	35
Issue number	9
DOIs	https://doi.org/10.1038/nbt.3947
Publication status	Published - 21 Aug 2017

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10.1038/nbt.3947

47537_3_merged_1501000692-1_accepted versionAccepted author manuscript, 2.27 MB

ISP1: Analysis and prediction in complex animal systems
Tenesa, A. (Principal Investigator), Archibald, A. (Co-investigator), Beard, P. (Co-investigator), Bishop, S. (Co-investigator), Bronsvoort, M. (Co-investigator), Burt, D. (Co-investigator), Freeman, T. (Co-investigator), Haley, C. (Co-investigator), Hocking, P. (Co-investigator), Houston, R. (Co-investigator), Hume, D. (Co-investigator), Joshi, A. (Co-investigator), Law, A. (Co-investigator), Michoel, T. (Co-investigator), Summers, K. (Co-investigator), Vernimmen, D. (Co-investigator), Watson, M. (Co-investigator), Wiener, P. (Co-investigator), Wilson, A. (Co-investigator), Woolliams, J. (Co-investigator), Ait-Ali, T. (Researcher), Barnett, M. (Researcher), Carlisle, A. (Researcher), Finlayson, H. (Researcher), Haga, I. (Researcher), Karavolos, M. (Researcher), Matika, O. (Researcher), Paterson, T. (Researcher), Paton, B. (Researcher), Pong-Wong, R. (Researcher), Robert, C. (Researcher) & Robertson, G. (Researcher)
BBSRC
1/04/12 → 31/03/17
Project: Research
A complete transcriptional map of the human body: systems Biology in toto (Japanese Partnering Grant)
Hume, D. (Principal Investigator), Freeman, T. (Co-investigator) & Summers, K. (Co-investigator)
BBSRC
1/10/11 → 30/09/14
Project: Research

Cite this

@article{5554d8acdb064a51b777cc98153cd74a,

title = "An integrated expression atlas of miRNAs and their promoters in human and mouse",

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",

author = "{The FANTOM Consortium} and {de Rie}, Derek and Amad Abugessaisa and Tanvir Alam and Erik Arner and Peter Arner and Haitham Ashoor and Gaby Astrom and Magda Babina and Nicolas Bertin and Burroughs, {A. Maxwell} and Carlisle, {Ailsa J.} and Daub, {Carsten O.} and Ruslan Deviatiiarov and Alexandre Fort and Claudia Gebhard and Daniel Goldowitz and Sven Guhl and Ha, {Thomas J.} and Jayson Harshbarger and Akira Hasegawa and Kosuke Hashimoto and Meenhard Herlyn and Peter Heutink and Hitchens, {Kelly J.} and Hon, {Chung Chau} and Edward Huang and Yuri Ishizu and Chieko Kai and Takeya Kasukawa and Peter Klinken and Timo Lassmann and Charles-Henri Lecellier and Weonju Lee and Marina Lizio and Makeev, {Vsevolod J} and Anthony Mathelier and Medvedeva, {Yulia A} and Niklas Mejhert and Mungall, {Christopher J} and Shohei Noma and Mitsuhiro Ohshima and Mariko Okada-Hatakeyama and Helena Persson and Patrizia Rizzu and Filip Roudnicky and Pal Saetrom and Hiroki Sato and Jessica Severin and Shin, {Jay W.} and Summers, {Kim M.}",

year = "2017",

month = aug,

day = "21",

doi = "10.1038/nbt.3947",

language = "English",

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journal = "Nature Biotechnology",

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AU - The FANTOM Consortium

AU - de Rie, Derek

AU - Abugessaisa, Amad

AU - Alam, Tanvir

AU - Arner, Erik

AU - Arner, Peter

AU - Ashoor, Haitham

AU - Astrom, Gaby

AU - Babina, Magda

AU - Bertin, Nicolas

AU - Burroughs, A. Maxwell

AU - Carlisle, Ailsa J.

AU - Daub, Carsten O.

AU - Deviatiiarov, Ruslan

AU - Fort, Alexandre

AU - Gebhard, Claudia

AU - Goldowitz, Daniel

AU - Guhl, Sven

AU - Ha, Thomas J.

AU - Harshbarger, Jayson

AU - Hasegawa, Akira

AU - Hashimoto, Kosuke

AU - Herlyn, Meenhard

AU - Heutink, Peter

AU - Hitchens, Kelly J.

AU - Hon, Chung Chau

AU - Huang, Edward

AU - Ishizu, Yuri

AU - Kai, Chieko

AU - Kasukawa, Takeya

AU - Klinken, Peter

AU - Lassmann, Timo

AU - Lecellier, Charles-Henri

AU - Lee, Weonju

AU - Lizio, Marina

AU - Makeev, Vsevolod J

AU - Mathelier, Anthony

AU - Medvedeva, Yulia A

AU - Mejhert, Niklas

AU - Mungall, Christopher J

AU - Noma, Shohei

AU - Ohshima, Mitsuhiro

AU - Okada-Hatakeyama, Mariko

AU - Persson, Helena

AU - Rizzu, Patrizia

AU - Roudnicky, Filip

AU - Saetrom, Pal

AU - Sato, Hiroki

AU - Severin, Jessica

AU - Shin, Jay W.

AU - Summers, Kim M.

PY - 2017/8/21

Y1 - 2017/8/21

N2 - 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

AB - 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

U2 - 10.1038/nbt.3947

DO - 10.1038/nbt.3947

M3 - Article

SN - 1087-0156

VL - 35

SP - 872

EP - 878

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 9

ER -

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

Abstract

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Projects

ISP1: Analysis and prediction in complex animal systems

A complete transcriptional map of the human body: systems Biology in toto (Japanese Partnering Grant)

Cite this