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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.

SUBMITTER: de Rie D 

PROVIDER: S-EPMC5767576 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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

de Rie Derek D   Abugessaisa Imad I   Alam Tanvir T   Arner Erik E   Arner Peter P   Ashoor Haitham H   Åström Gaby G   Babina Magda M   Bertin Nicolas N   Burroughs A Maxwell AM   Carlisle Ailsa J AJ   Daub Carsten O CO   Detmar Michael M   Deviatiiarov Ruslan R   Fort Alexandre A   Gebhard Claudia C   Goldowitz Daniel D   Guhl Sven S   Ha Thomas J TJ   Harshbarger Jayson J   Hasegawa Akira A   Hashimoto Kosuke K   Herlyn Meenhard M   Heutink Peter P   Hitchens Kelly J KJ   Hon Chung Chau CC   Huang Edward E   Ishizu Yuri Y   Kai Chieko C   Kasukawa Takeya T   Klinken Peter P   Lassmann Timo T   Lecellier Charles-Henri CH   Lee Weonju W   Lizio Marina M   Makeev Vsevolod V   Mathelier Anthony A   Medvedeva Yulia A YA   Mejhert Niklas N   Mungall Christopher J CJ   Noma Shohei S   Ohshima Mitsuhiro M   Okada-Hatakeyama Mariko M   Persson Helena H   Rizzu Patrizia P   Roudnicky Filip F   Sætrom Pål P   Sato Hiroki H   Severin Jessica J   Shin Jay W JW   Swoboda Rolf K RK   Tarui Hiroshi H   Toyoda Hiroo H   Vitting-Seerup Kristoffer K   Winteringham Louise L   Yamaguchi Yoko Y   Yasuzawa Kayoko K   Yoneda Misako M   Yumoto Noriko N   Zabierowski Susan S   Zhang Peter G PG   Wells Christine A CA   Summers Kim M KM   Kawaji Hideya H   Sandelin Albin A   Rehli Michael M   Hayashizaki Yoshihide Y   Carninci Piero P   Forrest Alistair R R ARR   de Hoon Michiel J L MJL  

Nature biotechnology 20170821 9


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 conservat  ...[more]

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