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 | |
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 | |
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 | |
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 | |
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 | |
FISSEQ (Fluorescent in situ sequencing) | Is a method, based on SOLiD sequencing, revealing spatial changes in lncRNAs during cancer | |
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. |