ChlRP (Chromatin lsolation by RNA Purification) is an experimental method to simultaneously analyze the interactions between IncRNA/circRNA, protein and DNA.
ChIRP-seq technique focuses on mapping genomic binding regions, detecting ncRNAs (e.g. lncRNA) and their protein binding sites on the genome, and quantitative and qualitative analysis of dna at binding sites. While ChIRP-MS focuses on the identification of RNA binding proteins (RBP).
Design of biotinylated oligomeric probes against target ncRNAs. Specifically hybridize ncRNA:RBPs:genomic dna complexes from cross-linked cell extracts. The complexes are purified with streptavidin magnetic beads. Target ncRNAs and associated dna are isolated using RNase H. Quantitative and qualitative analysis of associated dna is performed by deep sequencing and qPCR. Deep sequencing allows identification of lncRNA/protein interaction sites at single base resolution. ChIPR-seq offers the possibility to elucidate the complexity of ncrna regulatory events, which is essential for a better understanding of gene expression and disease pathogenesis.
As experts in the field of molecular interaction studies, Creative Proteomics offers ChIRP-Seq to identify the genomic binding regions (e.g., lncRNAs) where non-coding RNAs reside, as well as the bound proteins. ChIPR-seq offers the potential to elucidate the complexity of ncRNA regulatory events that are critical to better understanding gene expression and disease pathogenesis.
Our service is optimized for accuracy by:
IP group: Target IncRNA/circRNA Odd group and Even group (i.e. experimental group to identify IncRNA/circRNA action genomic location)
lacZ group: External reference control group to demonstrate the specificity of the ChlRP probe
Input group: Genomic DNA isolated and extracted before capture, used as an internal reference control group to demonstrate probe specificity
Positive group: Positive control group, to prove the validity of the whole ChlRP system by WB detection of known binding proteins with known validated probes
Target IncRNA/circRNA qPCR: Demonstrate the correct binding and effective capture of target IncRNA by ChlRP probes.
ChIRP-Seq analysis for Mrhl in mESCs (Pal et al., 2021)
Creative Proteomics can provide personalized assays for protein-RNA interactions, such as CLIP-seq, CHIP-Seq, and RIP-Seq services, according to customer needs, further providing powerful support for the study of complex regulatory mechanisms of RNA and even gene mediated expression in vivo.
Creative Proteomics has accumulated a wealth of experience in nucleic acid-protein interaction research. Our professional technical team can provide efficient ChIRP-Seq and many related features to our customers. Contact us to learn more.