ChIRP based RNA-Protein Interaction Analysis Service

Mapping Spatial RNA Regulatory Landscapes with Precision

At Creative Biolabs, we leverage cutting-edge ChIRP (Chromatin Isolation by RNA Purification) technology to decode the intricate spatial interactions between non-coding RNAs and their protein partners across the genome. Designed exclusively for preclinical research, our platform integrates proprietary hybridization capture, high-resolution sequencing, and AI-driven bioinformatics to deliver unparalleled insights into RNA-centric regulatory networks in disease biology, epigenetics, and target discovery.

Technology Overview: The ChIRP Advantage

ChIRP targets endogenous RNA molecules using tiled, biotinylated antisense oligonucleotides, enabling ultra-specific isolation of RNA-protein-chromatin complexes. This approach overcomes the limitations of traditional methods through:

• Spatial Specificity: Direct capture of architectural RNAs (e.g., lncRNAs, circRNAs) within native chromatin contexts.
• Multi-Omic Resolution: Simultaneous mapping of RNA-protein interactions and chromatin occupancy.
• Ultra-Low Background: Stringent washing eliminates non-specific binding, validated via scramble-oligo controls.

Featured Services

End-to-End Solutions - Comprehensive Service Offerings

Delivering modular, hypothesis-driven research packages to help you decode RNA-centric regulatory architectures.

• Endogenous Complex Isolation Service

We offer comprehensive support to capture native RNA-chromatin-protein interactions in situ, solving the critical challenge of preserving transient biological states. Our optimized workflows enable researchers to map physiological complexes with spatial fidelity, bringing unprecedented clarity to RNA-centric regulatory mechanisms.

• Architectural RNA Mapping Solutions

We deliver end-to-end expertise in profiling structural non-coding RNAs (e.g., scaffolding lncRNAs), addressing the technical hurdles of low-abundance target isolation. By implementing species-specific hybridization strategies, we help clients decode 3D genome organization mechanisms, accelerating discoveries in nuclear architecture and epigenetic reprogramming. This advances fundamental research in development and oncology.

• Dynamic Network Analysis Support

Our team provides specialized solutions for tracking RNA interactome rewiring across time-series or perturbation conditions. We overcome the limitations of static snapshots through rigorous longitudinal designs, enabling clients to reconstruct dynamic regulatory cascades in differentiation, stress response, or drug treatment models. This reveals transient therapeutic vulnerabilities inaccessible through conventional approaches.

Fig.1 ChIRP Service Workflow.

Advanced Bioinformatics

Our customizable analytical framework provides scalable computational insights:

Related RNA-Protein Interaction Services

Emerging Research Applications

1. lncRNA in 3D Genome Organization

• Architectural RNA Mechanisms
  Recent studies demonstrate how Xist and NEAT1 lncRNAs scaffold nuclear compartments, with spatial disruption linked to oncogenic gene activation.
• CRISPR-Guided Perturbation
  Combining ChIRP with dCas9-mediated lncRNA knockdown reveals compensatory chromatin rewiring in stem cell differentiation models.

2. Viral RNA-Host Interfaces

• Latency Regulation
  ChIRP-MS uncovered how Kaposi's sarcoma-associated herpesvirus (KSHV) lncRNA PAN recruits host ubiquitin ligases to evade immune surveillance.
• Therapeutic Target Screening
  High-throughput ChIRP identifies host dependency factors bound by SARS-CoV-2 regulatory RNAs.

3. Cancer Epigenetic Reprogramming

• Oncogenic lncRNA Circuits
  Integrated analysis of PVT1 revealed its role in stabilizing MYC protein at enhancer clusters, promoting chemoresistance in PDAC.
• Metastatic Niche Remodeling
  Tumor-derived lncRNAs (e.g., MALAT1) hijack nuclear matrix proteins to alter collagen architecture in pre-metastatic lungs.

4. Neurodevelopmental Dynamics

• Imprinted Loci Regulation
  Single-cell ChIRP uncovered cell-type-specific allelic silencing by Kcnq1ot1 lncRNA during cortical development.
• Phase Separation Pathology
  Aberrant FUS-RNA granules disrupt chromatin compartmentalization in ALS models, detectable via ChIRP-imaging fusion.

Partner with Creative Biolabs

Why Choose Us?

Deep Expertise

• 10+ years pioneering spatial RNA interactome research.
• We've successfully delivered 50+ non-coding RNA projects, empowering breakthroughs in nuclear architecture and disease mechanisms.

Innovation Leadership

• Proprietary approaches for unprecedented resolution.
• Overcome limitations of traditional methods with our optimized platform designed for complex biological contexts.

Pure Research Integrity

• 100% preclinical focus with zero therapeutic claims.
• Your data is generated under strict research ethics guidelines, ensuring publication-ready integrity.

Initiate Your Project

Share your target RNA, biological model (cell lines, organoids, or tissues), and research goals. Our specialists will provide:

• Customized oligo design strategy
• Tissue-specific protocol optimization
• Multi-omic integration roadmap

[Contact Us] Schedule a technical consultation within 24 hrs.

FAQs

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Reference

1. Mi, Xuelong, et al. "Fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signals." Cell 188.10 (2025): 2794-2809. Distributed under Open Access license CC BY-NC 4.0, without modification. https://doi.org/10.1016/j.cell.2025.03.012