An integrated expression atlas of miRNAs and their promoters in human and mouse
Authorsde Rie, Derek
Burroughs, A. Maxwell
Carlisle, Ailsa J.
Daub, Carsten O.
Ha, Thomas J.
Hitchens, Kelly J.
Hon, Chung Chau
Medvedeva, Yulia A.
Mungall, Christopher J.
Shin, Jay W.
Swoboda, Rolf K.
Zhang, Peter G.
Wells, Christine A.
Summers, Kim M.
Forrest, Alistair R. R.
de Hoon, Michiel J. L.
KAUST DepartmentComputer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Permanent link to this recordhttp://hdl.handle.net/10754/670083
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AbstractMicroRNAs (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.
CitationDe Rie, D., Abugessaisa, I., Alam, T., Arner, E., Arner, P., … Bertin, N. (2017). An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature Biotechnology, 35(9), 872–878. doi:10.1038/nbt.3947
SponsorsFANTOM5 was made possible by the following grants: Research Grant for RIKEN Omics Science Center from MEXT to Y.H.; Grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT to Y.H.; Research Grant from MEXT to the RIKEN Center for Life Science Technologies; Research Grant to RIKEN Preventive Medicine and Diagnosis Innovation Program from MEXT to Y.H. K.V.-S. and A.S. were supported by the Lundbeck and Novo Nordisk Foundations. A.R.R.F. is supported by a Senior Cancer Research Fellowship from the Cancer Research Trust, funds raised by the MACA Ride to Conquer Cancer, and the Australian Research Council’s Discovery Projects funding scheme (DP160101960). Y.A.M. was supported by the Russian Science Foundation, grant 15-14-30002. R.D. was supported by the Russian Science Foundation, grant 14-44-00022. We would like to thank L. Schwarzfischer for technical assistance and N. Eichner and G. Meister for sequencing RACE products. We would also like to thank GeNAS for data production.
PublisherSpringer Science and Business Media LLC
PubMed Central IDPMC5767576
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