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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; Åström, Gaby; Babina, Magda; Bertin, Nicolas and Burroughs, A. Maxwell, et al. (2017) In Nature Biotechnology 35(9). p.872-878
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... (More)

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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Nature Biotechnology
volume
35
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9
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7 pages
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Nature Publishing Group
external identifiers
  • scopus:85028474852
ISSN
1087-0156
DOI
10.1038/nbt.3947
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English
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yes
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bcd805d4-6bec-4e7a-bd28-fb2ae88c1c84
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2018-01-25 15:22:50
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@article{bcd805d4-6bec-4e7a-bd28-fb2ae88c1c84,
  abstract     = {<p>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.</p>},
  author       = {De Rie, Derek and Abugessaisa, Imad and Alam, Tanvir and Arner, Erik and Arner, Peter and Ashoor, Haitham and Åström, Gaby and Babina, Magda and Bertin, Nicolas and Burroughs, A. Maxwell and Carlisle, Ailsa J. and Daub, Carsten O. and Detmar, Michael and Deviatiiarov, Ruslan and Fort, Alexandre and Gebhard, Claudia and Goldowitz, Daniel and Guhl, Sven and Ha, Thomas J. and Harshbarger, Jayson and Hasegawa, Akira and Hashimoto, Kosuke and Herlyn, Meenhard and Heutink, Peter and Hitchens, Kelly J. and Hon, Chung Chau and Huang, Edward and Ishizu, Yuri and Kai, Chieko and Kasukawa, Takeya and Klinken, Peter and Lassmann, Timo and Lecellier, Charles Henri and Lee, Weonju and Lizio, Marina and Makeev, Vsevolod and Mathelier, Anthony and Medvedeva, Yulia A. and Mejhert, Niklas and Mungall, Christopher J. and Noma, Shohei and Ohshima, Mitsuhiro and Okada-Hatakeyama, Mariko and Persson, Helena and Rizzu, Patrizia and Roudnicky, Filip and Sætrom, Pål and Sato, Hiroki and Severin, Jessica and Shin, Jay W. and Swoboda, Rolf K. and Tarui, Hiroshi and Toyoda, Hiroo and Vitting-Seerup, Kristoffer and Winteringham, Louise and Yamaguchi, Yoko and Yasuzawa, Kayoko and Yoneda, Misako and Yumoto, Noriko and Zabierowski, Susan and Zhang, Peter G. and Wells, Christine A. and Summers, Kim M. and Kawaji, Hideya and Sandelin, Albin and Rehli, Michael and Hayashizaki, Yoshihide and Carninci, Piero and Forrest, Alistair R.R. and De Hoon, Michiel J.L.},
  issn         = {1087-0156},
  language     = {eng},
  month        = {09},
  number       = {9},
  pages        = {872--878},
  publisher    = {Nature Publishing Group},
  series       = {Nature Biotechnology},
  title        = {An integrated expression atlas of miRNAs and their promoters in human and mouse},
  url          = {http://dx.doi.org/10.1038/nbt.3947},
  volume       = {35},
  year         = {2017},
}