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; Kristoffer Vitting-Seerup; Albin Gustav Sandelin; FANTOM Consortium

doi:10.1038/nbt.3947

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 HarshbargerAkira 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, Kristoffer Vitting-Seerup, Albin Gustav Sandelin, FANTOM Consortium

Computational and RNA Biology

183 Citations (Scopus)

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.

Original language	English
Journal	Nature Biotechnology
Volume	35
Issue number	9
Pages (from-to)	872-878
Number of pages	7
ISSN	1087-0156
DOIs	https://doi.org/10.1038/nbt.3947
Publication status	Published - 1 Sept 2017

Keywords

Journal Article

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de Rie, D., Abugessaisa, I., Alam, T., Arner, E., Arner, P., Ashoor, H., Åström, G., Babina, M., Bertin, N., Burroughs, A. M., Carlisle, A. J., Daub, C. O., Detmar, M., Deviatiiarov, R., Fort, A., Gebhard, C., Goldowitz, D., Guhl, S., Ha, T. J., ... FANTOM Consortium (2017). An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature Biotechnology, 35(9), 872-878. https://doi.org/10.1038/nbt.3947

de Rie, D, Abugessaisa, I, Alam, T, Arner, E, Arner, P, Ashoor, H, Åström, G, Babina, M, Bertin, N, Burroughs, AM, Carlisle, AJ, Daub, CO, Detmar, M, Deviatiiarov, R, Fort, A, Gebhard, C, Goldowitz, D, Guhl, S, Ha, TJ, Harshbarger, J, Hasegawa, A, Hashimoto, K, Herlyn, M, Heutink, P, Hitchens, KJ, Hon, CC, Huang, E, Ishizu, Y, Kai, C, Kasukawa, T, Klinken, P, Lassmann, T, Lecellier, C-H, Lee, W, Lizio, M, Makeev, V, Mathelier, A, Medvedeva, YA, Mejhert, N, Mungall, CJ, Noma, S, Ohshima, M, Okada-Hatakeyama, M, Persson, H, Rizzu, P, Roudnicky, F, Sætrom, P, Sato, H, Vitting-Seerup, K, Sandelin, AG & FANTOM Consortium 2017, 'An integrated expression atlas of miRNAs and their promoters in human and mouse', Nature Biotechnology, vol. 35, no. 9, pp. 872-878. https://doi.org/10.1038/nbt.3947

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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.",

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AU - de Rie, Derek

AU - Abugessaisa, Imad

AU - Alam, Tanvir

AU - Arner, Erik

AU - Arner, Peter

AU - Ashoor, Haitham

AU - Åström, Gaby

AU - Babina, Magda

AU - Bertin, Nicolas

AU - Burroughs, A. Maxwell

AU - Carlisle, Ailsa J.

AU - Daub, Carsten O.

AU - Detmar, Michael

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

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 - Sætrom, Pål

AU - Sato, Hiroki

AU - Vitting-Seerup, Kristoffer

AU - Sandelin, Albin Gustav

AU - FANTOM Consortium

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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. 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.

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. 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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DO - 10.1038/nbt.3947

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SN - 1087-0156

VL - 35

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EP - 878

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 9

ER -

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

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