title: Insight into lncRNA biology using hybridization capture analyses.
abstract: Despite mounting evidence of the importance of large non-coding RNAs (lncRNAs) in biological regulation, we still know little about how these lncRNAs function. One approach to understand the function of lncRNAs is to biochemically purify endogenous lncRNAs from fixed cells using complementary oligonucleotides. These hybridization capture approaches can reveal the genomic localization of lncRNAs, as well as the proteins and RNAs with which they interact. To help researchers understand how these tools can uncover lncRNA function, this review discusses the considerations and influences of different parameters, (e.g., crosslinking reagents, oligonucleotide chemistry and hybridization conditions) and controls to avoid artifacts. By examining the application of these tools, this review will highlight the progress and pitfalls of studying lncRNAs using hybridization capture approaches.This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
authors.affiliation: Dept. of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06516, USA; Chemical Biology Institute, Yale West Campus, West Haven, CT, 06511, USA. Electronic address: matthew.simon@yale.edu.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Simon
mesh_terms: D000818:Animals; D002843:Chromatin / Q000235:genetics; D005786:Gene Expression Regulation; D016678:Genome; D009693:Nucleic Acid Hybridization / Q000235:genetics / Q000379:methods*; D016376:Oligonucleotides, Antisense / Q000737:chemistry / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000235:genetics*
chemical_list: D002843:Chromatin; D016376:Oligonucleotides, Antisense; D062085:RNA, Long Noncoding
keywords: CHART; ChIRP; Chromatin; Formaldehyde; Genomic localization; RAP; lncRNA