title: Detection and Analysis of Long Noncoding RNAs.
abstract: Recent genome-wide studies have yielded new insights into the biological function of long noncoding RNAs (lncRNAs), predominantly through analysis of their genomic addresses. These studies have revealed that a large number of lncRNAs map to regulatory elements in eukaryotic genome regions known as promoter and enhancer elements. Here, we review the principles of current methodologies for analyzing lncRNAs with high-throughput sequencing approaches. These include (1) direct RNA sequencing, (2) sequencing coupled with transcription, and (3) isolation of protein complexes associated with lncRNAs followed by high-throughput sequencing. Within these categories, we also describe detailed protocols for chromatin-associated RNA sequencing, nascent transcript Global run-on sequencing, and photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation.
authors.affiliation: Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States.
authors.forename: F
authors.initials: F
authors.lastname: Lai
authors.affiliation: Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States.
authors.forename: E
authors.initials: E
authors.lastname: Blumenthal
authors.affiliation: Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States. Electronic address: rshiekhattar@med.miami.edu.
authors.forename: R
authors.initials: R
authors.lastname: Shiekhattar
mesh_terms: D000818:Animals; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods; D062085:RNA, Long Noncoding / Q000032:analysis* / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D062085:RNA, Long Noncoding
keywords: Cap analysis of gene expression; Global run-on sequencing; Long noncoding RNA; Next-generation sequencing; Photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation; RNA immunoprecipitation and sequencing