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Table 2 Summary table of methods that have been developed to globally investigate ncRNAs conformation, relative activity of sites undergoing transcription, or half-life

From: Non-coding RNAs in cancer: platforms and strategies for investigating the genomic “dark matter”

TECHNIQUE BRIEF DESCRIPTION REF.
SHAPE (Selective 20-hydroxyl analysed by primer extension) Is a technique to unravel the secondary structure of lncRNAs [164,165,166]
PARS (Parallel analysis of RNA structure) Is a methods able to explore changes in lncRNAs structurome that can occurs in carcinogenesis, recently implemented with the Illumina platform (nextPARS) to provide results with higher throughput and sample multiplexing [167,168,169]
Frag-Seq (Fragmentation sequencing) Is an assay for probing RNA structure at transcriptome-wide level by combining RNA-seq and tools determining nuclease accessibility at single base resolution [99, 170, 171]
ICE-seq (Inosine chemical erasing sequencing) Is an approach able to reveal the deregulation that may occur in A-to-I editing of lncRNAs in cancer allowing relevant effect on their secondary structure and then, on the interaction with other RNA molecules [168, 172, 173]
BRIC-seq (50-bromo-uridine immunoprecipitation chase–deep sequencing) Is a method that determine precise RNA half life into cells in physiological and pathological conditions [174,175,176]
FISSEQ (Fluorescent in situ sequencing) Is a method, based on SOLiD sequencing, revealing spatial changes in lncRNAs during cancer [99, 177, 178]
Gro-seq (Global run-on assay sequencing) Is an NGS-based method that provide information about location, orientation and density of RNAs undergoing active transcription by RNA pol II. [174, 179, 180]