Chapter title |
High-Throughput Characterization of Primary microRNA Transcripts
|
---|---|
Chapter number | 1 |
Book title |
miRNA Biogenesis
|
Published in |
Methods in molecular biology, January 2018
|
DOI | 10.1007/978-1-4939-8624-8_1 |
Pubmed ID | |
Book ISBNs |
978-1-4939-8623-1, 978-1-4939-8624-8
|
Authors |
Tsung-Cheng Chang, Joshua T. Mendell, Chang, Tsung-Cheng, Mendell, Joshua T. |
Abstract |
Proper control of microRNA (miRNA) expression is critical for normal development and physiology, while abnormal miRNA expression is a common feature of many diseases. Dissecting mechanisms of miRNA regulation, however, is complicated by the generally poor annotation of miRNA primary transcripts (pri-miRNAs). Although some miRNAs are processed from well-defined protein coding genes, the majority of pri-miRNAs are poorly characterized noncoding RNAs, with incomplete annotation of promoters, splice sites, and polyadenylation signals. Due to the efficiency of DROSHA processing, the abundance of pri-miRNAs is very low at steady state, thereby complicating the elucidation of pri-miRNA structures. Here we describe a strategy to enrich intact pri-miRNAs and improve their coverage in RNA sequencing (RNA-seq) experiments. In addition, we outline a computational approach for reconstruction of pri-miRNA structures. This pipeline begins with raw RNA-seq reads and concludes with publication-ready visualization of pri-miRNA annotations. Together, these approaches allow the user to define and explore miRNA gene structures in a cell-type or organism of interest. |
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