High-throughput characterization of primary microRNA transcripts

Tsung Cheng Chang; Joshua T. Mendell

doi:10.1007/978-1-4939-8624-8_1

High-throughput characterization of primary microRNA transcripts

Tsung Cheng Chang, Joshua T. Mendell

Research output: Chapter in Book/Report/Conference proceeding › Chapter

3 Scopus citations

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.

Original language	English (US)
Title of host publication	Methods in Molecular Biology
Publisher	Humana Press Inc.
Pages	1-9
Number of pages	9
DOIs	https://doi.org/10.1007/978-1-4939-8624-8_1
State	Published - 2018

Publication series

Name	Methods in Molecular Biology
Volume	1823
ISSN (Print)	1064-3745

Keywords

Primary transcript
RNA-seq
Transcriptome assembly
microRNA
pri-miRNA

ASJC Scopus subject areas

Molecular Biology
Genetics

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10.1007/978-1-4939-8624-8_1

Cite this

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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.",

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author = "Chang, {Tsung Cheng} and Mendell, {Joshua T.}",

note = "Funding Information: We thank Steven Salzberg and Mihaela Pertea at Johns Hopkins University for assistance with design of the bioinformatic pipeline and Stephen Johnson at UT Southwestern for software implementation and computational support. This work was supported by grants from the Cancer Prevention and Research Institute of Texas (RP160249) and the National Institutes of Health (R35CA197311). J. T. M. is an Investigator of the Howard Hughes Medical Institute. Publisher Copyright: {\textcopyright} 2018, Springer Science+Business Media, LLC, part of Springer Nature.",

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AB - 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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High-throughput characterization of primary microRNA transcripts

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