Classification | Techniques | Short description | Strengths of the approach | Weakness | Ref |
---|---|---|---|---|---|
Microarrays | Tiling arrays | A method based on probes for discovering transcripts from specific genomic regions. | This approach can provide in-depth analysis of transcripts from target regions of genome. | Suffer from potential noise as a result of weak binding or cross-hybridization of transcripts to probes. | [56] |
Microarrays | A method based on a large number of oligonucleotide probes for performing quick global or parallel expression analysis of transcriptome. | Small size and high-throughput capabilities. | This method is not able to discover novel transcripts. | [57] | |
RNA-seq | RNA-seq | A technique that is currently the most widespread sequencing technology for both detecting RNA expression and discovering novel RNAs. | The method provides a global high-throughput detection amd identification of RNAs greater than 200 nt. | Its standard procedure is not suitable for detection of RNAs less than 200 nt. It also suffer from sequence errors at the reverse-transcription step or primer bias. | [58] |
RNA capture sequencing | A derivative technology combining RNA-seq with tilling arrays. | The method can specifically elevate the sequencing depth of target regions. | Suffer from disadvantages of both tiling arrays and RNA-seq. | [59] | |
scRNA-seq | Smart-seq | A scRNA-seq method based on a full-length cDNA amplification strategy. | Provide a full-length cDNA amplification of polyadenylated RNAs. | The limitations are lack of strand-specific identification, inability to read transcripts longer than 4 kb and only for polyadenylated RNAs. | [60] |
DP-seq | A scRNA-seq method using heptamer primers. | Suitable for smaller size samples or transcripts longer than 4 kb. this approach also suppresses highly expressed rRNAs in the cDNA library. | Captured RNAs are limited to polyadenylated RNAs. | [61] | |
Quartz-seq | A scRNA-seq method which reduces back ground noise. | Reduce background noise by using specially suppression PCR primers to reduce side products. | The method is limited to detecting polyadenylated RNAs. | [62] | |
SUPeR-seq | A single-cell universal polyadenylated tail-independent RNA sequencing. | Detect polyadenylated and nonpolyadenylated RNAs. Minimal rRNAs contamination. | Relatively low sensitivity for nonpolyadenylated RNAs. | [63] | |
RamDA-seq | A full-length total RNA-sequencing method for analyzing single cells. | High sensitivity for nonpolyadenylated RNAs. It can also uncover the dynamics of recursive splicing. | Unknown | [64] | |
Small RNA-seq | Small RNA-seq | A type of RNA-seq that discriminate small RNA from larger RNA to better evaluate and discover novel small RNAs. | Specifically detect and discover small or intermediate-sized RNAs with target sizes. | Adapter ligation bias lead to reverse transcription bias or amplification bias. | [65] |
Single-cell small-RNA sequencing | Small-seq | A method which detect small RNAs in a single cell. | The method can detect small RNAs in a single cell. | The limination may be similar to small RNA-seq. | [66] |
Nascent RNA-seq | GRO-seq | A method labeling nascent RNAs with 5Br-UTP and immunoprecipitating RNAs for sequencing. | Detect nascent RNAs and provide a genome-wide view of the location, orientation, and density of Pol II-engaged transcripts. | The method is confounded by contamination due to nonspecific binding, which could possibly result in experimental bias. | [67] |
SLAM-seq | A method distinguishing nascent RNA from total RNA via s4U-to-C conversion induced by nucleophilic substitution chemistry. | It is an enrichment-free method which can avoid contamination induced by affinity purification. | The oxidation condition caused certain oxidative damage to guanine, which may impact the accurancy of sequencing. | [68] | |
TimeLapse-seq | A method distinguishing nascent RNA from total RNA via s4U-to-C conversion induced by an oxidative nucleophilic aromatic substitution reaction. | It is an enrichment-free method which can avoid contamination induced by affinity purification. | The oxidation condition caused certain oxidative damage to guanine, which may impact the accurancy of sequencing. | [69] | |
AMUC-seq | A method distinguishing nascent RNA from total RNA via transforming s4U into a cytidine derivative using acrylonitrile. | More efficient and reliable because it has a minimal influence on the base-pairing manner of other nucleosides. | Unknown | [70] | |
Identification of RNA-chromatin interaction | GRID-seq | A method that aims to comprehensively detect and determine the localization of all potential chromatin-interacting RNAs. | Use a bivalent linker to ligate RNA to DNA in situ and provide exact profiles of RNA-chromatin interactome. | Usable sequence length for mapping RNA is 18–23 bp. However, short sequence length can result in ambiguity in mapping. | [71] |
iMARGI | A method providing a in situ mapping of RNA-genome interactome. | iMARGI needs less number of input cells and is suitable for paired-end sequencing. | Unknown | [72] | |
ChAR-seq | A chromatin-associated RNA sequencing that maps genome-wide RNA-to-DNA contacts. | Uncover chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs. | The method needs more than 100 million input cells. | [73] | |
Identification of RNA-RNA interaction | CLASH | A relatively early method that uses UV cross-linking to capture direct RNA-RNA hybridization. | Avoid noise from protein intermediate-mediated interactions. | This method only detects the RNA-RNA interactions base on proteins. | [74] |
RIPPLiT | A transcriptome-wide method for probing the 3D conformations of RNAs stably associated with defined proteins. | The method can capture 3D RNP structural information independent of base pairing. | This method only detects the RNA-RNA interactions base on proteins. | [75] | |
MARIO | A method identifying RNA-RNA interactions in the vicinity of all RNA-binding proteins using a biotin-linked reagent. | This method can identify RNA-RNA interactions in the vicinity of all RNA-binding proteins. | The method only detects the RNA-RNA interactions base on proteins. | [76] | |
PARIS | Psoralen analysis of RNA interactions and structures with high throughput and resolution. | Directly measure RNA-RNA interactions independent of proteins in living cells. | Unknown | [77] | |
LIGR-seq | A method for the global-scale mapping RNA-RNA interactions in vivo. | Provide global-scale mapping RNA-RNA interactions independent of proteins in vivo | Unknown | [78] | |
SPLASH | A method providing pairwise RNA-RNA partnering information genome-wide. | Map pairwise RNA interactions in vivo with high sensitivity and specificity, genome-wide. | Unknown | [79] | |
RIC-seq | RNA in situ conformation sequencing technology for the global mapping of intra- and intermolecular RNA-RNA interactions. | The method performs RNA proximity ligation in situ and can facilitate the generation of 3D RNA interaction maps. | Unknown | [80] | |
RNA proximity sequencing | A method based on massive-throughput RNA barcoding of particles in water-in-oil emulsion droplets. | This method can detect multiple RNAs in proximity to each other without ligation and is fit for studying the spatial organization of RNAs in the nucleus. | Unknown | [81] | |
RNAs in protein complexes or subcellular structures | FISSEQ | A method that offers in situ information of RNAs at high-throughput levels. | Provide information of RNAs at high-throughput levels. Visualization. | Unknown | [82] |
CeFra-seq | A method that physically isolates subcellular compartments and identifies their RNAs. | The methods have high sensitivity for low-abundance transcripts. | The method is limited to isolation protocols and the purity of resulting isolates. | [83] | |
APEX-RIP | A method can map organelle-associated RNAs in living cells via proximity biotinylation combined with protein-RNA crosslinking. | The technique can offer high specificity and sensitivity in targeting the transcriptome of membrane-bound organelles. | Unknown | [84] |