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 Astrom, 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 & 50 others 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, Pal Saetrom, 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

Research output: Contribution to journalArticle

78 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 languageEnglish
Pages (from-to)872–878
JournalNature Biotechnology
Volume35
Issue number9
DOIs
Publication statusPublished - Sep 2017

Cite this

de Rie, D., Abugessaisa, I., Alam, T., Arner, E., Arner, P., Ashoor, H., ... de Hoon, M. J. L. (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, Derek ; Abugessaisa, Imad ; Alam, Tanvir ; Arner, Erik ; Arner, Peter ; Ashoor, Haitham ; Astrom, Gaby ; Babina, Magda ; Bertin, Nicolas ; Burroughs, A. Maxwell ; Carlisle, Ailsa J. ; Daub, Carsten O. ; Detmar, Michael ; Deviatiiarov, Ruslan ; Fort, Alexandre ; Gebhard, Claudia ; Goldowitz, Daniel ; Guhl, Sven ; Ha, Thomas J. ; Harshbarger, Jayson ; Hasegawa, Akira ; Hashimoto, Kosuke ; Herlyn, Meenhard ; Heutink, Peter ; Hitchens, Kelly J. ; Hon, Chung Chau ; Huang, Edward ; Ishizu, Yuri ; Kai, Chieko ; Kasukawa, Takeya ; Klinken, Peter ; Lassmann, Timo ; Lecellier, Charles-Henri ; Lee, Weonju ; Lizio, Marina ; Makeev, Vsevolod ; Mathelier, Anthony ; Medvedeva, Yulia A. ; Mejhert, Niklas ; Mungall, Christopher J. ; Noma, Shohei ; Ohshima, Mitsuhiro ; Okada-Hatakeyama, Mariko ; Persson, Helena ; Rizzu, Patrizia ; Roudnicky, Filip ; Saetrom, Pal ; Sato, Hiroki ; Severin, Jessica ; Shin, Jay W. ; Swoboda, Rolf K. ; Tarui, Hiroshi ; Toyoda, Hiroo ; Vitting-Seerup, Kristoffer ; Winteringham, Louise ; Yamaguchi, Yoko ; Yasuzawa, Kayoko ; Yoneda, Misako ; Yumoto, Noriko ; Zabierowski, Susan ; Zhang, Peter G. ; Wells, Christine A. ; Summers, Kim M. ; Kawaji, Hideya ; Sandelin, Albin ; Rehli, Michael ; Hayashizaki, Yoshihide ; Carninci, Piero ; Forrest, Alistair R. R. ; de Hoon, Michiel J. L. / An integrated expression atlas of miRNAs and their promoters in human and mouse. In: Nature Biotechnology. 2017 ; Vol. 35, No. 9. pp. 872–878.
@article{a440b9ed7d674b118876533cbb01b582,
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. 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.",
keywords = "GENE-EXPRESSION, MICRORNA BIOGENESIS, SEQUENCING DATA, REGULATORY SITES, NONCODING RNAS, CAP-ANALYSIS, START SITES, TRANSCRIPTION, GENOME, CANCER",
author = "{de Rie}, Derek and Imad 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 Michael Detmar 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 Vsevolod Makeev 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 Swoboda, {Rolf K.} and Hiroshi Tarui and Hiroo Toyoda and Kristoffer Vitting-Seerup and Louise Winteringham and Yoko Yamaguchi and Kayoko Yasuzawa and Misako Yoneda and Noriko Yumoto and Susan Zabierowski and Zhang, {Peter G.} and Wells, {Christine A.} and Summers, {Kim M.} and Hideya Kawaji and Albin Sandelin and Michael Rehli and Yoshihide Hayashizaki and Piero Carninci and Forrest, {Alistair R. R.} and {de Hoon}, {Michiel J. L.}",
year = "2017",
month = "9",
doi = "10.1038/nbt.3947",
language = "English",
volume = "35",
pages = "872–878",
journal = "Nature Biotechnology",
issn = "1087-0156",
publisher = "Nature Publishing Group",
number = "9",

}

de Rie, D, Abugessaisa, I, Alam, T, Arner, E, Arner, P, Ashoor, H, Astrom, 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, Saetrom, P, Sato, H, Severin, J, Shin, JW, Swoboda, RK, Tarui, H, Toyoda, H, Vitting-Seerup, K, Winteringham, L, Yamaguchi, Y, Yasuzawa, K, Yoneda, M, Yumoto, N, Zabierowski, S, Zhang, PG, Wells, CA, Summers, KM, Kawaji, H, Sandelin, A, Rehli, M, Hayashizaki, Y, Carninci, P, Forrest, ARR & de Hoon, MJL 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

An integrated expression atlas of miRNAs and their promoters in human and mouse. / de Rie, Derek; Abugessaisa, Imad; Alam, Tanvir; Arner, Erik; Arner, Peter; Ashoor, Haitham; Astrom, Gaby; Babina, Magda; Bertin, Nicolas; Burroughs, A. Maxwell; Carlisle, Ailsa J.; Daub, Carsten O.; Detmar, Michael; Deviatiiarov, Ruslan; Fort, Alexandre; Gebhard, Claudia; Goldowitz, Daniel; Guhl, Sven; Ha, Thomas J.; Harshbarger, Jayson; Hasegawa, Akira; Hashimoto, Kosuke; Herlyn, Meenhard; Heutink, Peter; Hitchens, Kelly J.; Hon, Chung Chau; Huang, Edward; Ishizu, Yuri; Kai, Chieko; Kasukawa, Takeya; Klinken, Peter; Lassmann, Timo; Lecellier, Charles-Henri; Lee, Weonju; Lizio, Marina; Makeev, Vsevolod; Mathelier, Anthony; Medvedeva, Yulia A.; Mejhert, Niklas; Mungall, Christopher J.; Noma, Shohei; Ohshima, Mitsuhiro; Okada-Hatakeyama, Mariko; Persson, Helena; Rizzu, Patrizia; Roudnicky, Filip; Saetrom, Pal; Sato, Hiroki; Severin, Jessica; Shin, Jay W.; Swoboda, Rolf K.; Tarui, Hiroshi; Toyoda, Hiroo; Vitting-Seerup, Kristoffer; Winteringham, Louise; Yamaguchi, Yoko; Yasuzawa, Kayoko; Yoneda, Misako; Yumoto, Noriko; Zabierowski, Susan; Zhang, Peter G.; Wells, Christine A.; Summers, Kim M.; Kawaji, Hideya; Sandelin, Albin; Rehli, Michael; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R. R.; de Hoon, Michiel J. L.

In: Nature Biotechnology, Vol. 35, No. 9, 09.2017, p. 872–878.

Research output: Contribution to journalArticle

TY - JOUR

T1 - An integrated expression atlas of miRNAs and their promoters in human and mouse

AU - de Rie, Derek

AU - Abugessaisa, Imad

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 - 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 - Saetrom, Pal

AU - Sato, Hiroki

AU - Severin, Jessica

AU - Shin, Jay W.

AU - Swoboda, Rolf K.

AU - Tarui, Hiroshi

AU - Toyoda, Hiroo

AU - Vitting-Seerup, Kristoffer

AU - Winteringham, Louise

AU - Yamaguchi, Yoko

AU - Yasuzawa, Kayoko

AU - Yoneda, Misako

AU - Yumoto, Noriko

AU - Zabierowski, Susan

AU - Zhang, Peter G.

AU - Wells, Christine A.

AU - Summers, Kim M.

AU - Kawaji, Hideya

AU - Sandelin, Albin

AU - Rehli, Michael

AU - Hayashizaki, Yoshihide

AU - Carninci, Piero

AU - Forrest, Alistair R. R.

AU - de Hoon, Michiel J. L.

PY - 2017/9

Y1 - 2017/9

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.

KW - GENE-EXPRESSION

KW - MICRORNA BIOGENESIS

KW - SEQUENCING DATA

KW - REGULATORY SITES

KW - NONCODING RNAS

KW - CAP-ANALYSIS

KW - START SITES

KW - TRANSCRIPTION

KW - GENOME

KW - CANCER

U2 - 10.1038/nbt.3947

DO - 10.1038/nbt.3947

M3 - Article

VL - 35

SP - 872

EP - 878

JO - Nature Biotechnology

JF - Nature Biotechnology

SN - 1087-0156

IS - 9

ER -

de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H et al. An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature Biotechnology. 2017 Sep;35(9):872–878. https://doi.org/10.1038/nbt.3947