RACE-seq

RACE-sequencing (RACE-seq) refers to a method in molecular biology for characterizing cDNA molecules generated by Rapid amplification of cDNA ends using high-throughput sequencing technologies.
High-throughput sequencing characterization of RACE fragments is highly time-efficient, more sensitive, less costly and technically feasible compared to traditional characterization of RACE fragments with molecular cloning followed by Sanger sequencing of a few clones.

History and applications

RACE can be used to amplify unknown 5' (5'-RACE) or 3' (3'-RACE) parts of RNA molecules where part of the RNA sequence is known and targeted by a gene-specific primer. Combined with high-throughput sequencing for characterization of these amplified RACE products, it is possible to apply the approach to characterize any types of coding or non-coding RNA-molecules.

The idea of combining RACE with high-throughput sequencing was first introduced in 2009 as Deep-RACE to perform mapping of Transcription start sites (TSS) of 17 genes in a single cell-line.[1] In a study from 2014 to accurately map cleavage sites of target RNA directed by synthetic siRNAs, the approach was first named RACE-seq.[2] Further, the methodology was used to characterize full-length unknown parts of novel transcripts and fusion transcripts in colorectal cancer.[3] In another study aiming to characterize unknown transcript structures of lncRNAs, RACE was used in combination with semi-long 454 sequencing [4]

References

  1. ↑ Olivarius, S; Plessy, C; Carninci, P (February 2009). "High-throughput verification of transcriptional starting sites by Deep-RACE.". BioTechniques. 46 (2): 130–2. PMID 19317658.
  2. ↑ Denise, H; Moschos, SA; Sidders, B; Burden, F; Perkins, H; Carter, N; Stroud, T; Kennedy, M; Fancy, SA; Lapthorn, C; Lavender, H; Kinloch, R; Suhy, D; Corbau, R (4 February 2014). "Deep Sequencing Insights in Therapeutic shRNA Processing and siRNA Target Cleavage Precision.". Molecular therapy. Nucleic acids. 3: e145. PMID 24496437.
  3. ↑ Hoff, AM; Johannessen, B; Alagaratnam, S; Zhao, S; Nome, T; Løvf, M; Bakken, AC; Hektoen, M; Sveen, A; Lothe, RA; Skotheim, RI (3 November 2015). "Novel RNA variants in colorectal cancers.". Oncotarget. 6 (34): 36587–602. PMID 26474385.
  4. ↑ Lagarde, Julien; Uszczynska-Ratajczak, Barbara; Santoyo-Lopez, Javier; Gonzalez, Jose Manuel; Tapanari, Electra; Mudge, Jonathan M.; Steward, Charles A.; Wilming, Laurens; Tanzer, Andrea; Howald, Cédric; Chrast, Jacqueline; Vela-Boza, Alicia; Rueda, Antonio; Lopez-Domingo, Francisco J.; Dopazo, Joaquin; Reymond, Alexandre; Guigó, Roderic; Harrow, Jennifer (17 August 2016). "Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq)". Nature Communications. 7: 12339. doi:10.1038/ncomms12339.

External links

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