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

• Published in: Nature biotechnology Vol. 35; no. 9; pp. 872 - 878
• Main Authors: de Rie, Derek, Abugessaisa, Imad, Alam, Tanvir, Arner, Erik, Arner, Peter, Ashoor, Haitham, Åström, 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, Sætrom, Pål, 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
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.09.2017; Nature Publishing Group
• Subjects: 38/91; 45/91; 631/208/191/2018; 631/208/199; 631/208/514/1949; 631/337/384/331; Agriculture; Analysis; Animals; Basic Medicine; Biochemistry, Molecular Biology; Bioinformatics; Bioinformatik och systembiologi (metodutveckling under 10203); Biologi; Biologi (Medicinska tillämpningar under 3 och lantbruksvetenskapliga under 4); Biological Sciences; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Cages; Cell and Molecular Biology; Cell Biology; Cell- och molekylärbiologi; Cellbiologi; Cells, Cultured; Cellular biology; Conserved sequence; Gene expression; Gene Expression Profiling - methods; Gene Library; Gene sequencing; Genomes; Genomics; High-Throughput Nucleotide Sequencing; Humans; Libraries; Life Sciences; Mammalian cells; Mammals; Medical and Health Sciences; Medicin och hälsovetenskap; Medicinsk genetik; Medicinska och farmaceutiska grundvetenskaper; Methods; Mice; MicroRNA; MicroRNAs - genetics; MicroRNAs - metabolism; miRNA; Molecular Sequence Annotation; Natural Sciences; Naturvetenskap; Observations; Physiological aspects; Promoter Regions, Genetic - genetics; Promoters; resource; Ribonucleic acid; RNA; RNA sequencing; Rodents; Transcription; Wildlife conservation
• ISSN: 1087-0156; 1546-1696; 1546-1696
• DOI: 10.1038/nbt.3947

An atlas of microRNA expression patterns and regulators is produced by deep sequencing of short RNAs in human and mouse cells. 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.