RNA Antisense Purification

RAP isolates lncRNAs and maps the sequence of their target DNA through a probe-capture mechanism (Engreitz et al., 2013). First, the cells are crosslinked and lysed before DNase I chromatin digestion to 100_300 bp DNA fragments. Biotinylated RNA probes, antisense to the lncRNA, are hybridized and captured with streptavidin. The biotin-RNA probes are 120 nt and are tiled every 15 nt over the span of the lncRNA. The captured complexes are eluted and prepared for sequencing. RNA library preparation is done through RAP-RNA, and DNA library preparation by standard chromatin immuniprecipitation (ChIP).


  • Genomic mapping of lncRNA targets
  • Possible to sequence RNA and DNA from the purification products
  • Long RNA probe length provides high binding affinity to the target lncRNA (Kashi et al., 2015)
  • Minimal amplification steps during RNA sequencing after purification of the lncRNA complex


  • Requires the RNA sequence to be known


Illumina Library prep and Array Kit Selector


Kashi K., Henderson L., Bonetti A. and Carninci P. Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome. Biochim Biophys Acta. 2015;

Simon M. D. Insight into lncRNA biology using hybridization capture analyses. Biochim Biophys Acta. 2016;1859:121-127


Chen C. K., Blanco M., Jackson C., et al. Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing. Science. 2016;

Boque-Sastre R., Soler M., Oliveira-Mateos C., et al. Head-to-head antisense transcription and R-loop formation promotes transcriptional activation. Proc Natl Acad Sci U S A. 2015;

McHugh C. A., Chen C.-K., Chow A., et al. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature. 2015;521:232-236

Engreitz J. M., Sirokman K., McDonel P., et al. RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites. Cell. 2014;159:188-199