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

Citation: 
de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H,Åström 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, et al. An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature biotechnology. 2017;35(9):872-8.

Keywords: 
Animals, Cells, Cultured, Gene Expression Profiling/*methods, Gene Library, High, Throughput Nucleotide, Sequencing, Humans, Mice, MicroRNAs/*genetics/metabolism, *Molecular Sequence Annotation, Promoter Regions, Genetic/*genetics

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.