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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]