ChIRP-Seq Service

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, which is crucial to better understand gene expression and disease pathogenesis.

The overall scheme of ChIRP-Seq steps in detail as follows:

Services

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.

Our services are optimized for accuracy by:

• Reduced glutaraldehyde fixation time
• shorter shearing time
• Gentle shear conditions
• Better epitope preservation
• More sensitive IncRNA detection
• Tunable process

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.

Profacgen has accumulated lots of experience in nucleic acid-protein interaction research. Our professional technical team can provide customers with efficient ChIRP-Seq and many related featured services. Our competitive prices and extensive expertise have earned us the trust of our collaborators. Contact us to find out how Profacgen could be of assistance.

References

1. Chu, C.; et al. Chromatin Isolation by RNA Purification (ChIRP). J Vis Exp. 2012.
2. Chu, C.; et al. Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions. Mol. Cell. 2011.