Chromatin Isolation by RNA Purification (ChIRP)-MS Service

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Chromatin Isolation by RNA Purification (ChIRP)-MS Service

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CD BioSciences provides ChIRP service to detect plant proteins interacting with RNA, which can simultaneously analyze the interactions between lncRNA/circRNA, protein, and DNA. Combined with mass spectrometry, we can systematically and comprehensively identify plant proteins involved in transcriptional regulation.

The workflow of ChIRP-MS. Figure 1. The workflow of ChIRP-MS. (Chu, C., & Chang, H. Y., 2018)

ChIRP technology uses biotin probes that complement the target RNA sequence in reverse to pull down the target RNA, and the interacting fragments are attached to the streptavidin magnetic beads. Finally, the interacting proteins are identified by Western Blot and mass spectrometry.

Service Content

Service process

  • Probe design and check whether the probe sequence maps to a repeat sequence or other homologous transcripts.
  • Collection of cells for ChIRP experiments.
  • Sonication, keeping the average DNA length above 1-2 kb.
  • Probe hybridization, biotinylated oligonucleotides are hybridized to target RNA.
  • Proteins are extracted from ChIRP samples and identified by mass spectrometry or Western Blot.

Experimental group setting service

To ensure the accuracy and credibility of the experiment, we set up a variety of control groups.

Type Details Function
IP Group Target lncRNA/circRNA Odd group and Even group experimental group for identification of genomic locations of lncRNA/circRNA action.
lacZ group External reference control group To demonstrate the specificity of the ChIRP probe.
Input group Internal reference control group To prove the specificity of the probe.
Positive group Positive control group Proving the validity of the whole ChIRP experimental system by known verified valid probes and known binding proteins by Western Blot detection.
Target lncRNA/circRNA qPCR / Demonstrate the correct binding and effective capture of target lncRNA by ChIRP probes.

Sample Requirements

Cells > 107

Fresh plant tissue > 0.5g

RNA information, species information, and ID.

Technology Advantages

  • CHIRP experiments allow the study of cellular interactions in vivo.
  • CHIRP-MS experiments can be used to find proteins that bind to target lncRNAs without being limited by the length of the lncRNA.
  • Full-stranded probes are designed to cover the whole strand of lncRNA without being constrained by the complex structure of RNA.
  • Ultra-multi-site designed probes to specifically capture the target lncRNA binding site.
  • Self-mixing Probe Pool for multiple experimental reference combinations.

CD BioSciences is dedicated to screening plant proteins interacting with RNA. Our ChIRP-MS service combines ChIRP with mass spectrometry analysis to identify and characterize proteins associated with target genomic regions. If you have any questions, please feel free to contact us! We will enable you to gain insight into the protein composition of plant chromatin regions.

Reference

  1. Chu, C., & Chang, H. Y. (2018). ChIRP-MS: RNA-Directed Proteomic Discovery. Methods in molecular biology (Clifton, N.J.). 1861, 37-45.

For research use only, not for clinical use.