RNA-binding proteins (RBPs) are the essential master regulators that dictate the fate of RNA, from transcription and splicing to transport and translation. These protein-RNA interactions (RPIs) constitute a massive, dynamic regulatory network critical for maintaining cellular homeostasis. Creative Biolabs' RNA-Protein Interaction Analysis Services use advanced sequencing and phase separation analysis to map RPIs with high fidelity. We provide quantitative data for designing ASOs, small molecules, and gene-editing strategies, accelerating drug discovery.
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We offer a flexible suite of specialized services, each providing a distinct and powerful approach to characterizing the RNA-protein landscape based on your project goals:
| RIP-Seq based RNA-Protein Interaction Analysis | A foundational, antibody-based technique for identifying the general population of RNA targets associated with a specific RBP in a cellular context. It is ideal for initial screening and pathway mapping. |
| CLIP-Seq based RNA-Protein Interaction Analysis | Provides significantly higher resolution than RIP-seq, utilizing UV cross-linking to establish a covalent link between the RBP and its RNA target, allowing us to pinpoint exact binding sites at the nucleotide level. |
| ChIRP based RNA-Protein Interaction Analysis | Specifically designed to isolate long non-coding RNAs (lncRNAs) and identify their associated DNA and protein partners, revealing the lncRNA's full structural and functional network. |
| RAP based RNA-Protein Interaction Analysis | Utilizes antisense probes and highly denaturing conditions to capture specific RNA molecules and identify direct, high-confidence protein interactors. This technique is often coupled with Mass Spectrometry (RAP-MS) for comprehensive partner identification. |
| mRNA Interactome Capture (RIC) | A proteome-wide approach designed to covalently capture and identify all RNA-binding proteins within a cell or tissue lysate simultaneously, providing a holistic snapshot of the RBP landscape. |
Fig.1 RNA-centered RPI research methods include the in vitro incubation dropdown method, the ultraviolet cross-linking recovery method, and the proximity labeling method, etc.1,3
Our multi-modal platform ensures that every RPI is captured and analyzed under physiologically relevant conditions, providing data suitable for immediate translational application and designed for clear visualization as a flowchart.
Define project scope, target RBP, desired resolution, and specific LLPS/aggregation criteria. Leverage extensive experience to provide customized experimental design, including control strategies and sequencing depth recommendations.
Conduct physiologically relevant in vivo UV cross-linking to form irreversible covalent bonds between RBP and associated RNAs. Immediately follow with high-stringency purification (e.g., CARIC, RAP-MS) to isolate direct, stable RNP complexes and eliminate non-specific interactions.
Prepare next-generation sequencing (NGS) libraries or perform high-resolution mass spectrometry. Generate deep, accurate raw data for quantitative binding identification and comprehensive profiling of interacting partners.
Perform advanced computational analysis, including single-base resolution RBP binding site mapping, de novo motif discovery, and differential analysis (disease vs. healthy, treated vs. untreated). For LLPS projects, construct phase diagrams and model phase behavior using customized conditions to predict compound efficacy.
Provide in vitro validation of key RPIs (e.g., quantitative binding assays) and suggest optimized sequences for ASO or gene-editing guide design. Deliver a full project report with detailed findings, interpretations, and next-step recommendations.
As a leading partner in post-transcriptional therapeutics, Creative Biolabs provides a distinct competitive edge for expert biologists looking to accelerate their discovery pipeline. We offer robust, customizable solutions that transcend traditional RPI analysis.
Customized High-Resolution Mapping
Offer bespoke experimental designs for challenging targets, using CARIC, RAP-MS, or APEX-seq (superior to basic RIP-seq). Capture true physiological interactions and deliver single-base resolution data, even from complex or low-input samples.
Functional LLPS Quantification
Specializes in LLPS complex physics, providing quantitative phase diagram construction and compound screening via TriFC/FRET to modulate RNP condensates, supporting neurodegenerative drug discovery.
Mechanism-of-Action (MoA) Elucidation
Provide comprehensive analysis on how PTMs, mutations, or drug candidates affect RBP-RNA binding affinity and cellular function, furnishing data for regulatory submissions and IP protection.
End-to-End Scientific Partnership
Act as an extended research arm, offering expert consultation from target identification to functional validation and final reporting, ensuring scientific rigor and reproducible results throughout the project.
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By decomposing the interactions in the structural RNA-protein complex into those between residues and nucleotides. If there is a non-covalent interaction between the residue and the nucleotide, and the distance threshold is appropriate, it is considered that there is an interaction between them. RNA-protein interactions were also extracted from the database constructed based on high-throughput sequencing technology and the database constructed based on literature mining.
Fig.2 The workflow for building an RPI network.2,3
We primarily use advanced, high-resolution techniques like CLIP-seq variants and APEX-seq, which move beyond the general binding data of traditional methods. Our focus is on achieving single-base resolution and capturing interactions in vivo, ensuring the data reflects the true physiological context of the RNP complex and avoiding non-specific interactions.
Not at all. We are experts in the non-coding RNA world. We utilize specialized techniques like ChIRP and RAP to specifically map the protein and DNA interactions of long non-coding RNAs (lncRNAs) and circular RNAs, which are often key players in disease regulation but are notoriously difficult to purify and study.
Yes, functional validation is a core strength. We utilize sophisticated functional assays like Y3H and TriFC/FRET to screen compounds that disrupt or enhance a target RPI. Crucially, our LLPS modulation strategy allows us to quantitatively monitor if your lead compound can prevent pathological RBP aggregation or restore function, providing essential and translational MoA data for your drug development program.
We employ highly selective capture methods (e.g., affinity-based purification and specific cross-linking conditions) coupled with stringent bioinformatics filtering tailored to your organism. Furthermore, our APEX-seq proximity mapping delivers a clear, spatial picture of the RBP's local RNA interactome within a specific cellular compartment (like a stress granule or nucleus), allowing us to isolate its function from systemic noise or low-specificity binding.
Creative Biolabs delivers comprehensive RNA-Protein Interaction Analysis Services powered by advanced sequencing and functional LLPS analysis platforms. We provide the precise, translational data needed to accelerate drug discovery in oncology, neurodegeneration, and gene therapy.
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