Table 1.

Selected methods for functional lncRNA analysis.

Method	Reference
Determination of the intracellular lncRNA localization
Quantitative PCR (qPCR)	[34]
RNA-fluorescent in situ hybridization (RNA-FISH)	[35]
RNA-FISH combined with stochastic optical reconstruction microscopy (STORM)	[36]
lncRNA labeling with aptamers linked to fluorescent tags	[37,38]
lncRNA depletion or over-expression
Small interfering RNA (siRNA) silencing	[78,79]
Short hairpin RNA (shRNA) silencing	[80]
Antisense oligonucleotide (ASO) silencing	[79]
CRISPR/Cas9 knock-out/knock-in	[81]
The establishment of secondary and three-dimensional lncRNA structures
Shotgun secondary structure fragment analysis	[40]
Solution-state nuclear magnetic resonance (NMR) spectroscopy	[43,44]
Small-angle scattering (SAS)	[45]
X-ray diffraction and cryo-electron microscopy	[39]
Computational prediction	[41,42,46]
The determination of lncRNA-protein interactions (LPIs)
Cross-linking immunoprecipitation (CLIP)	[49,50]
Targets of RNA-binding proteins identified by editing (TRIBE)	[51]
Digestion-optimized RNA immunoprecipitation cDNA library sequencing (DO-RIP-seq)	[52]
RNA-affinity purification followed by mass spectrometry	[53,54,55,56]
RNA-affinity purification followed by protein microarrays	[57]
The isolation of target RNA molecules by biotinylated antisense probes	[54,58]
The isolation of target RNA molecules by peptide nucleic acid oligomers	[55]
HB-tag-based affinity RNA purification	[56]
Chromatin isolation with RNA purification (ChIRP)	[59,60]
RNA chromosome conformation capture (R3C)	[61]
LPI computational prediction	[72]
The biophysical characterization of quantitative and qualitative LPIs
Electrophoretic mobility shift assay (EMSA)	[62]
Filter-binding assays	[82]
Surface plasmon resonance	[63,64]
The evaluation of the coding capacity of lncRNAs
Ribosome profiling	[83]
Mass spectrometry	[84]
Global translation initiation sequencing (GTI-seq)	[73]