Identify where and how miRNAs and siRNAs bind

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miR-eCLIP provides actionable insights into miRNA and siRNA binding, learn how below.

miRNAs play significant roles in the regulation of RNA stability and translation, and siRNAs are an effective therapeutic modality for controlling RNA levels. Most methods for examining miRNA activity or identifying siRNA off-targets are indirect, relying on computational predictions or performing knockdown experiments. miR-eCLIP uses immunoprecipitation and ligation to directly identify where and how miRNAs and siRNAs bind.

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Map miRNA and siRNA binding

Typical species:

Human, mouse

Typical samples:

Cells, tissue

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Directly measure miRNA and siRNA binding

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

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The RISC complex and target RNA are crosslinked and immunoprecipitated


miRNAs and siRNAs are ligated to their targets and sequencing is performed


Custom bioinformatics analyses determine where and how miRNAs and siRNAs bind

Discover miRNA regulation and siRNA off-targets

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

Directly measure miRNA activity

Computational predictions are often used to identify miRNA activity, but the end result is a prediction that still requires validation. With miR-eCLIP, we use ligation to directly map where miRNAs are binding. This allows researchers to gain mechanistic insights into miRNA biology, and the developers of anti-miRs to validate that miRNA binding has been lost after treatment.

Direct detection of miRNA binding in the 3’ UTR of E2F3. Each row is a different miRNA. Peaks are where that specific miRNA binds.

Locate siRNA off-targets

siRNAs are an effective class of RNA therapeutics for regulating mRNA levels and treating disease. However, off-target binding can lead to clinical trial failure. With miR-eCLIP, we directly measure where and how siRNAs bind transcriptome-wide. When paired with eRibo Pro, our ribosome profiling technology, the effects of off-target binding on gene expression and translation can be determined as well. The results of these analyses provide siRNA developers with the data needed for candidate selection and siRNA optimization.

Validated siRNA off-target binding in the coding sequence of the gene COPRs. The siRNA was designed to target the gene APP.

Explore miRNA binding
with our K562 resource

We have used our miR-eCLIP technology to profile mRNA binding across the transcriptome in the K562 cell line. This deeply sequenced dataset can be used to discover novel regulatory programs, train AI models, and develop novel therapeutics.

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

miR-eCLIP reveals miRNA and siRNA binding, providing detailed information to understand RNA biology and develop more effective RNA therapeutics.

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