miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.
TLDR
For example, miRDeep2 as mentioned in this paper identifies canonical and non-canonical miRNAs such as those derived from transposable elements and informs on high-confidence candidates that are detected in multiple independent samples.Abstract:
microRNAs (miRNAs) are a large class of small non-coding RNAs which post-transcriptionally regulate the expression of a large fraction of all animal genes and are important in a wide range of biological processes. Recent advances in high-throughput sequencing allow miRNA detection at unprecedented sensitivity, but the computational task of accurately identifying the miRNAs in the background of sequenced RNAs remains challenging. For this purpose, we have designed miRDeep2, a substantially improved algorithm which identifies canonical and non-canonical miRNAs such as those derived from transposable elements and informs on high-confidence candidates that are detected in multiple independent samples. Analyzing data from seven animal species representing the major animal clades, miRDeep2 identified miRNAs with an accuracy of 98.6-99.9% and reported hundreds of novel miRNAs. To test the accuracy of miRDeep2, we knocked down the miRNA biogenesis pathway in a human cell line and sequenced small RNAs before and after. The vast majority of the >100 novel miRNAs expressed in this cell line were indeed specifically downregulated, validating most miRDeep2 predictions. Last, a new miRNA expression profiling routine, low time and memory usage and user-friendly interactive graphic output can make miRDeep2 useful to a wide range of researchers.read more
Citations
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Circular RNAs are a large class of animal RNAs with regulatory potency
Sebastian Memczak,Marvin Jens,Antigoni Elefsinioti,Francesca Torti,Janna Krueger,Agnieszka Rybak,Luisa Maier,Sebastian D. Mackowiak,Lea H. Gregersen,Mathias Munschauer,Alexander Loewer,Ulrike Ziebold,Markus Landthaler,Christine Kocks,Ferdinand le Noble,Nikolaus Rajewsky +15 more
TL;DR: It is found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7.
Conflict of interest statement. None declared.
TL;DR: It is found that women over 50 are more likely to have a family history of diabetes, especially if they are obese, than women under the age of 50.
Journal ArticleDOI
Characterization of human plasma-derived exosomal RNAs by deep sequencing
Xiaoyi Huang,Tiezheng Yuan,Michael Tschannen,Zhifu Sun,Howard J. Jacob,Meijun Du,Meihua Liang,Rachel L. Dittmar,Yong Liu,Mingyu Liang,Manish Kohli,Stephen N. Thibodeau,Lisa A. Boardman,Liang Wang +13 more
TL;DR: This study demonstrated that a wide variety of RNA species are embedded in the circulating vesicles and suggested that the highly abundant miRNAs may play an important role in biological functions such as protein phosphorylation, RNA splicing, chromosomal abnormality, and angiogenesis.
Journal ArticleDOI
Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function
Monika Piwecka,Petar Glažar,Luis R. Hernandez-Miranda,Sebastian Memczak,Susanne A. Wolf,Agnieszka Rybak-Wolf,Andrei Filipchyk,Filippos Klironomos,Cledi Alicia Cerda Jara,Pascal Fenske,Thorsten Trimbuch,Vera Zywitza,Mireya Plass,Luisa Schreyer,Salah Ayoub,Christine Kocks,Ralf Kühn,Christian Rosenmund,Carmen Birchmeier,Nikolaus Rajewsky +19 more
TL;DR: It is suggested that neuronal Cdr1as stabilizes or transports miR-7, which in turn represses genes that are early responders to different stimuli, and that CDR1as modulates neuronal activity in the human brain.
Journal ArticleDOI
An overview of microRNAs: Biology, functions, therapeutics, and analysis methods
TL;DR: Altered of miRNAs following exercise, their association with diseases, and therapeutic potential will be explained, and miRNA bioinformatics tools and conventional methods for miRNA detection and quantification will be discussed.
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