As an expert in the field of studying protein-nucleic acid interactions, Profacgen provides a powerful technique, Chromatin isolation by RNA purification followed by sequencing analysis (ChIRP-Seq), which has been widely used for identifying the genomic binding regions where the noncoding RNAs (e.g., lncRNA) of interest, and their RBPs are bound.
The introduction of RIP-ChIP/Seq
In eukaryotic organisms, a tight regulation of gene expression is required for complex biological processes such as development, differentiation, cell specification, and response of each cell to environmental signals. However, noncoding RNAs (e.g., lncRNA) as key regulators play a role in these biological processes via different mechanisms including RNA-protein interactions, RNA-RNA interactions and RNA-DNA interactions.
ChIRP-seq is a powerful in vivo, high-throughput technique for mapping genomic binding regions, which are bound by the ncRNAs of interest and their RBPs. The basic idea is that to design the biotinylated oligo probes against the ncRNA of target, which is used to specifically hybridize ncRNAs:RBPs:genomic DNAs complex from cell extracts after crosslinking, then the purification of this complex using streptavidin magnetic beads, followed by isolation of the ncRNA of target and associated DNAs using RNase A and H, quantitative and qualitative analysis for associated DNAs using deep sequencing and qPCR analysis. ChIPR-seq provides the possibility to shed light on the complexity of ncRNAs regulatory events is crucial to better understand gene expression and disease pathogenesis.
A workflow of ChIRP-Seq
The overall scheme of ChIRP-Seq steps in detail as follows:
Figure 1. Diagram of Basic Protocol of ChIRP-Seq
The Merits of ChIRP-Seq
Compared with conventional methods and technology, ChIRP-Seq has become increasingly more favored by the researchers because of its own a variety of advantages, including:
Significantly, based on the customer requirements, Profacgen could also provide personalized testing services on protein-RNA interactions, like CLIP-seq, CHIP, RIP-Seq services, to further provide strong support for studying the complex regulation mechanism mediated by RNAs and even gene expression in vivo.