Rajan Tavathia and Cynthia Dillon, SDSC Communications, contributed to this story.
University of California President Postdoctoral Fellow Edwin Solares used ACCESS allocations at San Diego Supercomputer Center (SDSC) at UC San Diego to complete a project as part of his mission to help address the growing concern of food insecurity. His work focused on the study of genomic features in maize and resulted in the discovery of tiny ribonucleic acid (RNA), as explained in a paper published in the journal Genome Research.
“In this long-term study, we first used Comet to run tens of millions of simulations – looking at how RNA works within individual maize genes,” said Solares, a lecturer and researcher with the UC San Diego Computer Science and Engineering Department. “We ran our sims using ACCESS allocations at SDSC and then switched to a cluster I built at UC Irvine, where I was working at the time.”
Solares said that the team’s simulations of RNA “folding” of various genes, junk DNA, randomized DNA and other genomic features led to a surprising discovery.
“Previous work in this arena focused on ancient viral infections called ‘sireviruses,’ where DNA from the virus was inserted into the genome, was duplicated across the whole genome, and showed that the RNA produced from these ancient viral domains, degrades and creates a specific size RNA due to formation of what we call ‘secondary structure (folding in on itself),’ and regulates and even sometimes shuts down that machinery, effectively silencing it,” Solares explained. “In our study, we saw the same presence of these small RNA that most likely came from sireviruses, but also other ancient viral infections and other repetitive areas – what was the most interesting finding was the presence of tiny RNA from genes!”
Solares said that this discovery was made possible by ACCESS allocations and, more importantly, was not expected. He said that the origins of this mechanism – the degradation and cutting into these size fragments – are still unknown, as is the function. He said that now his focus with his ACCESS allocations is to examine these small RNA to see if they’re from genes or ancient viral and repetitive domains.
“Was it co-opted into genes, or was it co-opted into repeats and ancient viral infections?” Solares asked. “We aren’t quite sure, but we will next use ACCESS resources to better understand this phenomenon and look forward to continuing our work with the center.”
See the original story here: Supercomputing Simulations in Multiyear Study of Corn to Address Food Insecurity Reveal Surprising Molecular Results
Project Details
Resource Provider Institution(s): San Diego Supercomputer Center (SDSC)
Affiliations: University of California
Funding Agency: NSF
Grant or Allocation Number(s): MCB180035
The science story featured here was enabled by the U.S. National Science Foundation’s ACCESS program, which is supported by National Science Foundation grants #2138259, #2138286, #2138307, #2137603, and #2138296.