RNA immunoprecipitation chip

A RNA immunoprecipitation chip (RIP-Chip) is immunoprecipitation of an RNA-binding protein coupled to reverse transcription and a microarray. It has been used to find interactions between RNA and protein (one protein but many RNA species per analysis).[1][2][3]

RIP-Seq

An alternative methodology (RIP-Seq) is to sequence the RNAs that were pulled down using high-throughput sequencing rather than analyze them with a microarray.

ChIP-on-chip

A similar technique is ChIP-on-chip, which detects the binding of proteins to genomic DNA rather than RNA.

CLIP-Seq

A competing technique is CLIP-Seq, where the RNA binding protein is cross-linked to the RNA via the use of UV light, followed by nuclease digestion and analyzed with high-throughput sequencing.

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References
  1. Townley-Tilson WH, Pendergrass SA, Marzluff WF, Whitfield ML (October 2006). "Genome-wide analysis of mRNAs bound to the histone stem–loop binding protein". RNA. 12 (10): 1853–67. doi:10.1261/rna.76006. PMC 1581977. PMID 16931877.
  2. Khalil AM, Guttman M, Huarte M, et al. (July 2009). "Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression" (PDF). Proc. Natl. Acad. Sci. U.S.A. 106 (28): 11667–72. doi:10.1073/pnas.0904715106. PMC 2704857. PMID 19571010.
  3. Hendrickson DG, Hogan DH, Herschlag D, Ferrell JEF, Brown PB (2008). Bähler J (ed.). "Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance". PLoS ONE. 3 (5): e2126. doi:10.1371/journal.pone.0002126. PMC 2330160. PMID 18461144.


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