Building a database around RNA and proteins

eCLIP technology helps uncover how RNA binding proteins regulate gene expression

November 25, 2020
Mel J. Yeates

SAN DIEGO—Eclipse Bioinnovations Inc. has reported the publication of a large dataset of RNA-binding protein interactomes, which will help to provide a foundation for understanding human diseases caused by failed RNA processing.

The study, published in Nature, was led by University of California, San Diego (UC San Diego) scientists and Eclipse co-founders Drs. Gene Yeo and Eric Van Nostrand, in collaboration with international researchers.

“RNA is emerging as a key and yet under-appreciated aspect of nearly all human diseases,” states Yeo, who is professor of cellular and molecular medicine at UC San Diego School of Medicine. “This work provides the first big-picture glimpse at the full regulatory map of how RNAs are processed and controlled in human cells, which is the first step towards being able to truly understand how modification of RNA processing can drive such a wide array of diseases throughout the body.”

Researchers used enhanced crosslinking and immunoprecipitation (eCLIP) technology to match hundreds of these RNA binding proteins to the internal instructions on RNA.

“To be able to generate such a large dataset of RNA-binding protein target maps, a technology was needed that was robust and able to scale, as prior CLIP technologies often required significant per-experiment optimization that made such a large-scale effort impossible,” Van Nostrand notes. “The development of eCLIP enabled a thousand-fold improvement in recovery of RNA, decreasing experimental failures and enabling us to use paired controls to remove common background seen in previous methods.”

“This work, which generated more than 10 terabytes of data in just 36 months, represents a tour de force made possible only by the unique combination of cell and molecular biology, biochemistry, and advanced computational analysis rolled into the highly efficient, reproducible, and robust eCLIP technology,” added Dr. Peter Chu, cofounder and CEO of Eclipse.

The dataset has revealed that RNA binding proteins act like tiny “smart sensors” to decode and carry out instructions that determine the RNA’s levels and locations within the cell. This impacts how the cell functions in both healthy and disease states.

“With the growing excitement in the RNA therapeutics field, understanding how RNAs are controlled in healthy and also diseased cells is important for the safe development of new therapeutics,” says Yeo. “This unbiased view of targets for 150 RNA binding proteins reveal general principles of how RNAs are controlled. We are excited that researchers worldwide are already utilizing these datasets to drive new insights into how altered RNA processing drives human diseases.”

“This dataset includes in-vivo RNA target interactome profiling for 150 RNA binding proteins across two human cancer cell lines, the largest such effort to date,” Van Nostrand tells DDN. “This was generated with the eCLIP method, which is a recently described technology to isolate an RNA binding protein along with the RNA targets it binds to within cells or tissues, and use high-throughput sequencing and computational analysis to read out these RNA ‘binding sites’ throughout the transcriptome.”

“We now know that mutation or altered expression of many RNA binding proteins is a key driver of disease, and for proteins in this dataset, the interactomes can give insight into the mechanisms of how these proteins drive disease,” continues Van Nostrand. “In addition, we are starting to see researchers in other fields beginning to incorporate this data as well—for example, overlaying the interaction sites we see in RNA transcripts with mutations from genome sequencing efforts in order to predict which mutations are most likely to be functional in driving disease phenotypes.”

The eCLIP technology was initially developed by Yeo and Van Nostrand at UC San Diego, and is licensed to Eclipse Bioinnovations. Eclipse has developed the base eCLIP technology from UC San Diego into a commercially successful service and kit product. The company has also expanded the eCLIP platform to offer miRNA and m6A RNA modification products.

“There are already many researchers using these datasets to explore basic research into RNA biology, studying functions of individual RNA binding proteins as well as broader views of RNA processing, and we expect the usage of this dataset in RNA biology will continue to expand as more researchers gain familiarity with it,” continues Yeo. “Also, as genome sequencing continues to become more common, datasets such as these provide an incredible resource to try to understand which polymorphisms lie in regulatory regions, enabling clinicians and researchers to decide which are important to focus on for follow-up studies and the development of potential targeted therapies.”

“We believe the data reported in this study will provide a useful framework for understanding other key aspects of RNA regulation, such as miRNA processing, RNA modifications, translational efficiency and RNA editing,” Van Nostrand concludes.

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