Map where proteins bind across the transcriptome

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Our RBP-eCLIP technology directly reveals where and how proteins bind, learn how below.

All RNAs in the cell are bound by proteins, and these RNA-binding proteins (RBPs) play significant roles in health, disease, and developing successful RNA therapeutics. Over 1500 RBPs have been identified that play critical roles in RNA splicing, stabilization, localization and translation. Understanding how and where they act is critical for therapeutic development and basic research.

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Map protein binding sites

Typical species:

Human, mouse, rat

Typical samples:

Cells, tissues

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Locate where and how proteins bind

Ready to start your RBP-eCLIP project? Contact us today.

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Crosslinked protein and RNA complexes are immunoprecipitated with a selective antibody


Libraries are prepared and next-generation sequencing is performed


Custom bioinformatics analyses determine where and how proteins bind

Discover protein binding biology

The following are some examples of the types of insights that RBP-eCLIP can provide. For our partners, we perform additional analyses to provide actionable insights for therapeutic success.

Transcriptome-wide identification of protein targets

RBP-eCLIP provides an unbiased examination of where proteins bind, revealing binding in introns, exons, UTRs, and non-coding targets such as lncRNAs. These results can be used to obtain a deeper understanding of RNA biology, identify optimal UTRs for mRNA therapeutics, or discover targetable proteins for small molecule drugs.

Browser tracks showing where different RNA-binding proteins bind to the gene WSB1.

Reveal how proteins bind

RBPs can bind to specific sequences (called motifs) or to specific structures. With standard RBP-eCLIP, our comprehensive analysis includes the identification of enriched sequencing motifs, allowing for the discovery of novel binding patterns. When paired with eSHAPE, our technology for determining RNA secondary structure, structural binding motifs can also be identified.

Browser tracks for RBFOX2, an RBP that binds to introns at UGCAUG motifs. The location of identified UGCAUG motifs is highlighted.

Screen mRNA therapeutics

We have developed a custom database of RBP motifs that we use to identify potential sites of RBP regulation on mRNA therapeutics. Available as a part of eMERGE, our RNA characterization and optimization platform, this analysis provides therapeutic developers with potential regulatory regions that can be optimized to reduce or enhance binding.

Heatmap showing the location of identified RBP motifs along an mRNA vaccine. Each teal tick is where a known binding motif was located.

Explore ENCODE-validated protein binding with our community resource

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Contact us today to start a project with our team of RNA experts.

RBP-eCLIP reveals how and where proteins bind, providing detailed information to understand RNA biology and develop more effective RNA therapeutics.

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