@inbook{496a77ff0951437696c621e5dac639e4,
title = "High-throughput characterization of primary microRNA transcripts",
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.",
keywords = "Primary transcript, RNA-seq, Transcriptome assembly, microRNA, pri-miRNA",
author = "Chang, {Tsung Cheng} and Mendell, {Joshua T.}",
note = "Publisher Copyright: {\textcopyright} 2018, Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2018",
doi = "10.1007/978-1-4939-8624-8_1",
language = "English (US)",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "1--9",
booktitle = "Methods in Molecular Biology",
}