SAN DIEGO, Aug. 11, 2020 /PRNewswire/ — Eclipse Bioinnovations, an RNA genomics company that helps scientists accelerate RNA research and medicines, celebrates the publication of the largest dataset of RNA-binding protein-interactomes, which provides a foundation for understanding human diseases caused by failed RNA processing. The study was published in Nature and led by UC San Diego scientists and Eclipse cofounders Gene Yeo, Ph.D., and Eric Van Nostrand, Ph.D., in collaboration with international researchers.
RNA is the intermediary between the DNA code in every cell and the specific set of proteins that are expressed in each cell that carry out life’s functions. Major scientific questions have been where and how instructions within RNA affects the eventual proteins that emerge. The dataset revealed extensive, previously hidden information about how 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 in turn drives how the cell functions in healthy and disease states, driving new potential therapeutic interventions.
However, there are thousands of different RNA binding proteins and millions of RNAs, so identifying which instructions are being read by which RNA binding protein is a crucial challenge. To address this, researchers used eCLIP technology to match hundreds of these RNA binding proteins to the internal instructions on RNA.
“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 Dr. Yeo, professor of cellular and molecular medicine at UC San Diego School of Medicine. “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.”
“We at Eclipse are excited to see the eCLIP platform technology in action to provide the most comprehensive maps of RBPs to date,” says Eclipse CEO and cofounder Peter Chu, Ph.D. “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.”
The eCLIP technology, enhanced crosslinking and immunoprecipitation followed by sequencing, was initially developed by Drs. Yeo and Van Nostrand at UC San Diego and is licensed to Eclipse Bioinnovations (Nature Methods, 2016). Since 2017, Eclipse has further developed the base eCLIP technology from UC San Diego into a commercially successful service and kit product. Eclipse has also expanded the eCLIP platform to offer miRNA and m6A RNA modification products.
Dr. Van Nostrand said, “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.”
The paper entitled, “A large-scale binding and functional map of human RNA-binding proteins,” is available open access on Nature as part of a special package of 10 studies from the Encyclopedia of DNA Elements (ENCODE) Consortium. ENCODE is an international collaboration led by the National Human Genome Research Institute (NHGRI) to build a comprehensive parts list to understand how genes are controlled.
The ENCODE Project began in 2003 and is an extensive collaborative research effort involving groups across the U.S. and internationally, comprising over 500 scientists with diverse expertise. It has benefited from and built upon decades of research on gene regulation performed by independent researchers around the world. ENCODE researchers have created a community resource, ensuring that the project’s data is accessible to any researcher for their studies. These efforts in open science have resulted in over 2,000 publications from non-ENCODE researchers who used data generated by the ENCODE Project. For more info, visit www.encodeproject.org.