人类和小鼠中miRNA及其启动子的综合表达图谱。
An integrated expression atlas of miRNAs and their promoters in human and mouse.
作者信息
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
机构信息
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam, the Netherlands.
出版信息
Nat Biotechnol. 2017 Sep;35(9):872-878. doi: 10.1038/nbt.3947. Epub 2017 Aug 21.
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.
微小RNA（miRNA）是在细胞调控中起关键作用的短链非编码RNA。作为哺乳动物基因组功能注释（FANTOM5）项目第五版的一部分，我们通过对来自396个人类和47个小鼠RNA样本的492个短RNA（sRNA）文库进行深度测序，并结合相应的帽分析基因表达（CAGE）数据，创建了一个miRNA及其启动子的综合表达图谱。确定了1357个人类和804个小鼠miRNA的启动子，并显示出物种间的强序列保守性。我们还发现初级和成熟miRNA的表达水平相关，这使我们能够在总共1829个人类和1029个小鼠CAGE文库中，将初级miRNA测量值用作成熟miRNA水平的替代指标。因此，我们提供了一个关于原代哺乳动物细胞中miRNA表达和启动子的广泛图谱，为详细分析miRNA表达模式和转录控制区域奠定了基础。
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