ChiRP-Seq Service

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).

Principle and Process of ChiRP-Seq

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.

Advantages of ChiRP-Seq

• In Vivo Technology
• High throughput
• Suitable for a variety of eukaryotic cells
• Identifies binding sites anywhere on the genome
• Enables discovery of new binding sites
• Allows selection of specific RNAs of interest
• Flexible experimental design. Enables assays and systematic analysis of different components (ncRNAs, RBPs and genomic DNA)

ChiRP-Seq Service in Creative Proteomics

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:

• Reduced glutaraldehyde fixation time
• Shorter shearing times
• Milder shearing conditions
• Better epitope preservation
• More sensitive IncRNA detection
• Adjustable process

Experimental grouping of ChlRP-seq

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.