CLIP-Seq based RNA-Protein Interaction Analysis Service

Mapping RNA Regulatory Networks with Subcellular Precision

Creative Biolabs uses our advanced CLIP-Seq (Cross-Linking and Immunoprecipitation Sequencing) technology to provide insights into RNA-binding interactions across the transcriptome. By harnessing our proprietary crosslinking techniques, high-fidelity immunoprecipitation, and AI-powered bioinformatics, we deliver confident and precise binding maps tailored exclusively for preclinical applications in transcriptomics, disease biology, and target identification.

Technology Overview: The CLIP-Seq Advantage

CLIP-Seq captures physiological RNA-protein interactions through UV-induced covalent crosslinking, followed by target-specific immunoprecipitation and deep sequencing. This approach overcomes the limitations of traditional methods by:

• True in vivo binding: UV crosslinking "freezes" transient interactions within live cells, preserving authentic binding sites.
• Single-nucleotide resolution: Advanced pipelines pinpoint binding motifs with base-level accuracy.
• Reduced false positives: Rigorous RNase digestion eliminates non-bound RNA fragments, enhancing signal-to-noise ratios.

Featured Services

Comprehensive CLIP-Seq Workflow

We deliver modular research solutions spanning experimental design to biological interpretation:

Fig.1 CLIP-Seq Service Workflow.

Advanced Bioinformatics

Our customizable analytical framework provides scalable computational insights:

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Emerging Research Applications for CLIP-Seq

1. miRNA Target Deconvolution

• Multi-omics integration redefines validation paradigms
  Converging experimental perturbation data (e.g., miRNA knockout/overexpression) with computational predictions has uncovered clinically relevant regulatory hubs. In oncology, integrated approaches recently revealed miR-30a-mediated cell cycle control through CDC7-DBF4 targeting, with target expression correlating with patient survival outcomes.
• Single-cell resolution unlocks cellular heterogeneity
  Recent advancements in single-cell pri-miRNA mapping in plants uncovered cell-type specific regulatory networks (e.g., miR858a repressing MYB transcription factors in vascular cell pri-miRNAs), opening up new avenues for tissue-specific mechanism studies.

2. Splicing Machinery Dynamics

• Splice factors as immuno-oncology targets
  Recent genome-wide CRISPR screening revealed the splice factor PTPN2 as a negative regulator of antitumor immunity, implicating the splicing machinery in the modulation of tumor microenvironment cross-talk.
• 3D genome-splicing interplay
  Spatial chromatin organization coordinates with splice factor recruitment (e.g., SF3B1 at TAD boundaries), where disruption of architectural proteins alters exon selection patterns in neural development models.

3. RNA-Centric Disease Mechanisms

• Nuclear morphology as mechanistic biomarker
  Aberrant TDP-43/FUS aggregation induces quantifiable nuclear envelope alterations in neurodegeneration models, detectable via AI-enhanced imaging approaches.
• Multi-scale regulatory hierarchies
  Recent studies reveal that certain RBPs maintain local chromatin stability despite global structural disruption, suggesting layered regulatory mechanisms.

• Targeting cancer stemness vulnerabilities
  RBP-RNA interactions (e.g., LIN28/IGF2BP-MYC axis) sustain tumor-initiating cell properties, with disruption showing synergistic effects with conventional therapies.
• Metabolic reprogramming interfaces
  RNA-binding proteins increasingly emerge as post-transcriptional regulators of cancer metabolism, influencing therapeutic response pathways.

4. CRISPR-Guided RBP Perturbation

• Physiological context screening
  Organoid-AAV hybrid platforms now enable RBP functional screening in near-physiological environments, revealing regeneration-associated chromatin remodelers.
• Multi-modal perturbation phenotyping
  Simultaneous genomic architecture and transcriptome profiling following gene perturbation identifies novel 3D genome regulators (e.g., CHD7 deletion reducing compartment interactions).

Partner with Creative Biolabs

Why Choose Us?

• End-to-End Expertise:10+ years in RNA-protein interaction studies, from optimized protocols to publication-ready data visualization
• Technology Leadership:Pioneers in implementing high-resolution interaction capture methodologies with continuous innovation
• Preclinical Integrity:100% research-focused services—strictly for mechanistic exploration, zero therapeutic claims

Initiate Your Project

Share your target RBP, biological model, and research objectives with our specialists to receive a tailored proposal, including experimental design recommendations and analytical strategy. Contact our team to schedule a technical consultation and accelerate your research.

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References

1. Zhang, Zijun, and Yi Xing. "CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome." Nucleic acids research 45.16 (2017): 9260-9271. Distributed under Open Access license CC BY-NC 4.0, without modification. https://doi.org/10.1093/nar/gkx646
2. Li, Yang Eric, et al. "Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA–protein binding sites." Genome biology 18 (2017): 1-16. Distributed under Open Access license CC BY 4.0, without modification. https://doi.org/10.1186/s13059-017-1298-8