Comprehensive study of UCSC-developed RNA reader appears in Nature Methods

Two generations of Oxford Nanopore Technologies MinION
James McGirk

Oxford Nanopore Technologies’s palm-sized DNA and RNA sequencer, the MinION, has been used in Africa during the Ebola epidemic, orbited above planet earth in the International Space Station, and can be found analyzing samples in laboratories all over the world.

The nanopore device allows scientists to rapidly determine the precise chemical composition of a single molecule of DNA or RNA—the molecules encoding all life on earth—by reading its sequence, or its unique series of base pairs. The technology behind the MinION, called “nanopore sequencing,” was developed at UC Santa Cruz in the 1990s. The original idea was invented by David Deamer, research professor in the Baskin School of Engineering.

It is particularly useful for looking at the structure of RNA — DNA’s “messenger molecule”— which delivers coded instructions from the DNA molecule to the protein-creating ribosomes.

On November 18, 2019 Nature Methods published “Nanopore native RNA sequencing of a human poly(A) transcriptome,” the results of a multi-university consortium’s investigation into the benefits and areas needing further improvement of this brand new method of RNA sequencing.

It is a new way to analyze RNA, and this paper was a comprehensive look at this increasingly influential platform.

“The nanopore device allows investigators to look at individual molecules of RNA directly. Most techniques for looking at RNA make a DNA copy, and then you use that DNA copy to infer what the RNA strand was made of.

“One advantage of this new method is that you can see modifications on the RNA that affect many of its properties,” said UC Santa Cruz Professor Mark Akeson.

Akeson is a tenured professor of bioengineering at the Baskin School of Engineering and was a corresponding author of the Nature Methods article along with Professor Winston Timp of Johns Hopkins University. The study involved researchers from the UC Santa Cruz Genomics Institute and RNA Center, Johns Hopkins University, University of Toronto, Ontario Institute for Cancer Research, University of British Columbia, University of Birmingham and the University of Nottingham.

“This was the first comprehensive independent look at this technique,” Akeson said. “There were some features that were really strong. For instance, nanopores can document modifications to RNA and read individual strands from end to end. The longest strand we detected was on the order of 21,000 nucleotide, which is extraordinary. There were also areas that need to be fixed. For example, we saw that the electronic signal sometimes artificially truncates the RNA reads.”

Dr. Miten Jain and Dr. Hugh Olsen, Research Scientists in UC Santa Cruz’s Nanopore Group, accounted for much of the detailed analysis of base call performance. Alison Tang and Cameron Soulette, currently bioinformatics graduate students in Angela Brooks’ Lab, helped develop an algorithm called FLAIR that allowed investigators to assemble isoforms of RNA and overcome some of the errors present in the nanopore reads. Benedict Paten, Assistant Professor, helped direct the bioinformatics component of the study.

Being able to detect modifications along individual strands will offer a substantially more detailed view of how RNA structure and composition can affect function and development of biological cells.

The study was funded by the U.S. Department of Health & Human Services, NIH, | National Human Genome Research Institute (NHGRI); Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada); RCUK | Medical Research Council (MRC); U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI); RCUK | Biotechnology and Biological Sciences Research Council (BBSRC); Ontario Institute for Cancer Research (Institut Ontarien de Recherche sur le Cancer); U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)