Map Direct microRNA (miRNA) Interactions

miR-eCLIP

High Resolution Maps of the miRNA-mRNA Interactome

Technology Overview

miR-eCLIP™ enables precise mapping of direct miRNA-mRNA interactions transcriptome-wide and can also be utilized to look at off-targets of siRNA. In contrast to alternative techniques that provide indirect methods to map miRNA targets (i.e., computational algorithms or over-expression/knockdown experiments), miR-eCLIP identifies direct in vivo miRNA targets using AGO2 immunoprecipitation, RNA-RNA ligation, and high-throughput sequencing (similar to methods such as CLASH or CLEAR-CLIP). Further, miR-eCLIP has the option of enriching for specific miRNAs or genes of interest, enabling profiling of miRNA-target interactions at an unprecedented depth.

Precise microRNA (miRNA) target identification is essential to understand post-transcriptional gene regulation. With more than 2000 miRNAs in the human genome, miRNA regulation has been shown to be involved in nearly every physiological system and miRNA misregulation is linked to human diseases; however, identification of the mRNA targets of miRNAs remains a critical challenge.

Technology Highlights

Direct Detection of microRNA Targets

miR-eCLIP utilizes a modified AGO2-eCLIP protocol to enhance ligation of miRNAs to target mRNAs yielding miRNA-mRNA chimeric fragments
miR-eCLIP on human cells results in thousands of miRNA-mRNA chimeric reads that can be utilized for direct miRNA target identification

Reveal Functional microRNA Targets

miR-eCLIP reveals functional miRNA target genes that are predominantly downregulated in corresponding RNA-seq experiments
miR-eCLIP quantitatively characterizes the strength of each target interaction yielding increased miRNA-mRNA chimeric read coverage on genes with increased repression levels in corresponding RNA-seq experiments
miR-eCLIP identifies fewer false positive targets than purely computational predictions from tools like TargetScan

miR-eCLIP +miR: Distinct Target Profiling for microRNAs of Interest

Enrich samples for miRNA-mRNA chimeric reads specific to miRNA(s) of interest to deeply profile target repertoire of miRNAs of varying abundance
Enrich for entire miRNA families to resolve targets of miRNA family members

miR-eCLIP +Gene: Comprehensive Profiling of microRNA Binding Sites for a Gene of Interest

miR-eCLIP +Gene can maximize data coverage increasing the number of chimeric miRNA-mRNA reads on a transcript of interest 50 to 300-fold
Deeper coverage enables the identification of additional miRNAs targeting the gene of interest

Direct Detection of microRNA Targets

miR-eCLIP utilizes a modified AGO2-eCLIP protocol to enhance ligation of miRNAs to target mRNAs yielding miRNA-mRNA chimeric fragments
miR-eCLIP on human cells results in thousands of miRNA-mRNA chimeric reads that can be utilized for direct miRNA target identification

Reveal Functional microRNA Targets

miR-eCLIP reveals functional miRNA target genes that are predominantly downregulated in corresponding RNA-seq experiments
miR-eCLIP quantitatively characterizes the strength of each target interaction yielding increased miRNA-mRNA chimeric read coverage on genes with increased repression levels in corresponding RNA-seq experiments
miR-eCLIP identifies fewer false positive targets than purely computational predictions from tools like TargetScan

miR-eCLIP +miR: Distinct Target Profiling for microRNAs of Interest

Enrich samples for miRNA-mRNA chimeric reads specific to miRNA(s) of interest to deeply profile target repertoire of miRNAs of varying abundance
Enrich for entire miRNA families to resolve targets of miRNA family members

miR-eCLIP +Gene: Comprehensive Profiling of microRNA Binding Sites for a Gene of Interest

miR-eCLIP +Gene can maximize data coverage increasing the number of chimeric miRNA-mRNA reads on a transcript of interest 50 to 300-fold
Deeper coverage enables the identification of additional miRNAs targeting the gene of interest