RPIs regulate transcriptome and gene expression, critical for health and disease. CLIP-Seq uses in vivo UV crosslinking to capture native RPIs, sequences RNA fragments for single-nucleotide resolution, aiding novel drug target identification in oncology and infectious disease. Creative Biolabs' CLIP-Seq service uses advanced coCLIP and proprietary ML to accelerate drug discovery, provide high-resolution compartment-specific RPI mapping, and deliver high-confidence data for rational drug design and target validation.
Discover How We Can Help - Request a Consultation
The RPI network is the "dark matter" of the genome—vast, critical, and hard to measure due to the transient nature of RNA-protein bonds. Creative Biolabs' service directly addresses the two main challenges: resolution (low-resolution methods lose critical detail) and context (conventional CLIP loses spatial information). Our platform ensures that the captured interactions are not only high-resolution but also biologically relevant to the specific cellular compartment or disease state being studied.
Fig.1 The basic steps of the HITS-CLIP, PAR-CLIP, and vPAR-CL methods contained in CLIP.1
Our process is meticulously structured to provide clear milestones, ensuring transparency and quality control at every stage.
Consult with clients to select the optimal CLIP variant (coCLIP, PAR-CLIP, eCLIP) and define the target RBP/cell line. Conduct quality assessment of the provided antibodies and cells.
For coCLIP projects, perform APEX2 proximity labeling before UV crosslinking. Covalently link the RBP to its RNA targets in vivo within the specified cellular compartment.
Execute stringent immunoprecipitation of RBP-RNA complexes, followed by radio-labeling, gel electrophoresis, size selection, and specialized library preparation to capture CIMS signatures.
Map raw sequencing data to the genome. Use proprietary algorithms to identify CIMS locations and define high-confidence binding peaks (clusters).
Apply Creative Biolabs' ML models to filtered, high-confidence data to score, rank, and predict the functional impact and exact interacting segments of non-coding RNAs.
Creative Biolabs delivers the gold standard in RNA-Protein Interaction analysis. Our customized CLIP-Seq based RNA-Protein Interaction Analysis Service is engineered by molecular biology experts to provide you with the most biologically relevant and actionable data, saving you time and resources in your critical discovery phases.
Customized CLIP Strategy
Protocol tailored specifically to your target RBP's expression level (low-abundance → CLIP), affinity, and project scope, ensuring maximal data yield and quality.
Unmatched Subcellular Precision
Exclusive utilization of Colocalization CLIP (coCLIP) to resolve RPIs in the nucleus, cytosol, or specialized bodies like stress granules, overcoming the limitations of conventional, bulk analysis.
Molecular Fingerprinting Guarantee
Rigorous use of the Crosslink-Induced Mutation Site (CIMS) signature to ensure the mapped sites are direct, high-confidence RBP binding locations at single-nucleotide resolution.
Predictive Validation Roadmap
Integration of proprietary Machine Learning (ML) to turn raw sequencing data into a prioritized, ranked list of therapeutic targets and their precise binding segments for immediate downstream validation.
Specialized LncRNA Expertise
Optimized protocols and computational analysis for successfully mapping RPIs involving challenging, low-abundance non-coding RNAs, broadening your target landscape.
Application-Specific Protocol Development
Dedicated services for engineering therapeutic molecules by mapping RBP interactions to optimize mRNA stability and translation efficiency.
Expert Quality Control
Decades of experience in molecular biology applied to every step, from RBP antibody validation to deep, functional data interpretation, far exceeding standard core facility output.
Experience the Creative Biolabs Advantage - Get a Quote Today
We combine the high cost of experimental CLIP-Seq with proprietary Machine Learning prediction. This predictive intelligence drastically reduces your downstream experimental validation costs, as you only test the highest-confidence, ML-prioritized targets. It transforms a single experiment into an entire drug development roadmap.
Absolutely. Our Colocalization CLIP (coCLIP) technology is specifically designed to overcome this limitation. We can map your RBP's targets with subcellular precision, revealing how its binding preferences and functional roles change based on its exact location.
LncRNAs are a primary focus. By integrating highly sensitive CLIP variants (like eCLIP) and powerful computational analysis, we effectively analyze low-abundance non-coding RNA data. More importantly, our ML component is trained to predict the minimal lncRNA binding segment, simplifying your follow-up functional assays.
While we can advise on cell line and conditions, the most critical factor is the quality and specificity of the RBP antibody. We include a rigorous quality control check on the antibody before starting to ensure robust and reliable immunoprecipitation, as antibody failure is the most common reason for low-yield data.
RIP-Seq is a low-resolution method that only confirms that an RBP and an RNA exist in the same complex. Our CLIP-Seq methods, especially PAR-CLIP and eCLIP, provide single-nucleotide resolution via the CIMS signature, allowing you to pinpoint the exact sequence of the interaction site—essential for designing small-molecule disruptors.
Creative Biolabs offers the most comprehensive, high-resolution, and actionable RPI mapping platform available. Our integrated approach—combining world-class NGS techniques like coCLIP with proprietary Machine Learning—translates complex biological data into a clear, validated, and accelerated path for therapeutic development. Don't let the "dark matter" of RPIs slow your progress.
Contact Our Team for More Information and to Discuss Your Project
Reference
