On January 17, 2023 Eclipse Bioinnovations (Eclipsebio), a leading RNA genomics company developing and commercializing novel, data-driven technologies that interrogate RNA, reported its new research demonstrating the optimization of Eclipsebio’s industry-standard eCLIP technology to improve the study of RNA-binding protein interactomes, which promises to accelerate the study of human diseases caused by failed RNA processing (Press release, Eclipse Bioinnovations, JAN 17, 2023, View Source [SID1234626322]). The study, published in Nature Methods, was led by Eclipsebio’s Associate Director of Research Daniel Lorenz, Ph.D., and co-founder Gene Yeo, Ph.D.

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"Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP"

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Enhanced cross-linking immunoprecipitation followed by high-throughput sequencing, or eCLIP, is a powerful technique to uncover RNA sequences where RNA-binding proteins (RBPs) bind, known as RBP interactomes. RBPs regulate RNA molecules, controlling the function and quantity of proteins expressed in a cell. RBP mutations have been associated with cancer, amyotrophic lateral sclerosis, and a number of other diseases.

"eCLIP is a powerful technique that scientists utilize to study disease samples with RBP mutations, and this optimized antibody-barcode eCLIP (ABC) technology will allow a faster and more efficient study of RBP interactomes to gain new insights into novel disease targets and therapeutics," said Eclipsebio CEO and cofounder Peter Chu, Ph.D. "ABC is designed to optimize the study of RNA-binding protein interactomes in clinically relevant samples, including disease tissues, where source materials are rare and often scarce."

In this published study, Eclipsebio and UC San Diego scientists developed the ABC methodology that bypasses electrophoresis and membrane transfer and allows the study of interactomes of more than one RBP in the same reaction tube, which will support small sample volumes and sizes.

"We proved that ABC methodology maintains a comparable sensibility and specificity to eCLIP while improving the number of RBP interactomes that can be studied in one reaction tube," explained Dr. Yeo. "We showed that a single ABC library obtained from one reaction tube generates similar data to ten separate eCLIP experiments."

During eCLIP, there is an immunoprecipitation (IP) step, where an antibody against the RBP of interest is used to "grab" the binding RNA. In ABC, the IP step allows using more than one antibody in the same reaction tube, where each antibody is tagged with a different DNA barcode. After the IP step, a multiplex reverse transcriptase (RT) reaction identifies to which one of the RBP antibodies the RNA sequences were bound since the DNA barcode used serves as a primer for the RT reaction.

Dr. Chu concluded, "The Eclipsebio team is committed to developing the leading technologies to accelerate the study of RNA regulation, and this study opens the door to even further scaling. By increasing the number of barcodes used in each reaction tube, more interactomes could be studied simultaneously. We look forward to supporting important RBP research with our current and future eCLIP products that will include the ABC technology."

The publication entitled, "Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP," is available open access on Nature Methods.

About Eclipsebio’s RNA Genomics Platform and Products

Eclipsebio’s comprehensive RNA genomics platform is poised to build the world’s most detailed multi-dimensional RNA maps through transcriptome-wide views of RNA interactions with RNA binding proteins (RBP-eCLIP), RNA modifications such as m6A (m6A-eCLIP), alternative transcription start site and polyadenylation site usage (EndSeq), and microRNA-mRNA interactions (miR-eCLIP). Upcoming products in development are designed to profile translation (eRibo) and probe RNA structure