RIP-chip (RNA immunoprecipitation chip) is a molecular biology technique which combines RNA immunoprecipitation with a microarray. The purpose of this technique is to identify which RNA sequences interact with a particular RNA binding protein of interest in vivo. [1] [2] [3] [4] It can also be used to determine relative levels of gene expression, to identify subsets of RNAs which may be co-regulated, or to identify RNAs that may have related functions. [4] [5] This technique provides insight into the post-transcriptional gene regulation which occurs between RNA and RNA binding proteins. [5]
The genes fluorescently identified by the chip analysis are the genes whose RNA interacts with the original protein of interest. The strength of the fluorescent signal for a particular gene can indicate how much of that particular RNA was present in the original sample, which indicates the expression level of that gene.
Previous techniques aiming to understand protein-RNA interactions included RNA Electrophoretic Mobility Shift Assays and UV-crosslinking followed by RT-PCR, [9] however such selective analysis cannot be used when the bound RNAs are not yet known. [1] To resolve this, RIP-chip combines RNA immunoprecipitation to isolate RNA molecules interacting with specific proteins with a microarray which can elucidate the identity of the RNAs participating in this interaction. [5] [1] Alternatives to RIP-chip include: