Biologists pioneer first method to decode gene expression

August 12, 2019

Given the recent remarkable advancements in genetics, it's easy to assume that 21st century scientists have at their disposal a clear, quick way to run a genomic sequence scan and find out which genes among thousands can be expressed and which cannot. Gene expression is the process by which information encoded within genes leads to key products, such as proteins.

Surprisingly, that hasn't been possible until now. Biologists at the University of California San Diego have developed the first system for determining gene expression based on machine learning. Given the lack of such a method, the new process is considered a type of genetic Rosetta Stone for biologists.

"This paper represents the first method to distinguish genes that can be expressed from those that cannot," said Steve Briggs, a Division of Biological Sciences professor and senior author of the paper. "This is the basis for all of biology. Whether it's drug discovery or plant breeding or evolution, this touches the basic studies of biology."

The method, developed by graduate student Ryan Sartor, Briggs and their colleagues, is described August 12, 2019 in the Proceedings of the National Academy of Sciences.

Biologists have previously classified gene expression through experimental observations and scientific literature references. But the genomics field lacked a formalized process for revealing this information, called the "expressible gene set," or EGS, which comprises all protein-coding genes with the potential to be expressed.

"In biology, there is no method to do this," said Briggs. "In the past we've just had empirical approaches to making catalogs--we haven't had scientific criteria that classifies the genes based on their molecular features."

The new method leverages machine learning, the use of algorithms and other processes to analyze data, and is based on an example set of nearly 30,000 maize plant genes containing specific, detailed molecular features. An advanced algorithm was trained on the data and "learned" to classify gene expression at 99.4 percent accuracy.

The key to the advancement is bringing together chromatin biology, which contributes to regulating the DNA packaging within cells, with molecular features that are known to determine gene expression. Combining these with mathematical machine learning, the new method of determining the species-wide set of transcribed genes, or "expressome," then creates an atlas of expressible genes. The method may also be useful in understanding evolutionary mechanisms that silence certain genes.

Briggs is now applying the method to sorghum, an important grain for food and fodder, but says it can be useful beyond plant species. Ultimately, he says the new method is like a word decoder.

"The genome sequence is like a book," said Briggs. "The words are the genes. Until now, we couldn't tell which DNA sequences were real words and which merely resembled words. By removing non-words we now have a much more accurate reading of the book."
-end-
Coauthors of the paper include Jaclyn Noshay and Nathan Springer of the University of Minnesota. The National Science Foundation's Plant Genome Research Program supported the research.

University of California - San Diego

Related Science Articles from Brightsurf:

75 science societies urge the education department to base Title IX sexual harassment regulations on evidence and science
The American Educational Research Association (AERA) and the American Association for the Advancement of Science (AAAS) today led 75 scientific societies in submitting comments on the US Department of Education's proposed changes to Title IX regulations.

Science/Science Careers' survey ranks top biotech, biopharma, and pharma employers
The Science and Science Careers' 2018 annual Top Employers Survey polled employees in the biotechnology, biopharmaceutical, pharmaceutical, and related industries to determine the 20 best employers in these industries as well as their driving characteristics.

Science in the palm of your hand: How citizen science transforms passive learners
Citizen science projects can engage even children who previously were not interested in science.

Applied science may yield more translational research publications than basic science
While translational research can happen at any stage of the research process, a recent investigation of behavioral and social science research awards granted by the NIH between 2008 and 2014 revealed that applied science yielded a higher volume of translational research publications than basic science, according to a study published May 9, 2018 in the open-access journal PLOS ONE by Xueying Han from the Science and Technology Policy Institute, USA, and colleagues.

Prominent academics, including Salk's Thomas Albright, call for more science in forensic science
Six scientists who recently served on the National Commission on Forensic Science are calling on the scientific community at large to advocate for increased research and financial support of forensic science as well as the introduction of empirical testing requirements to ensure the validity of outcomes.

World Science Forum 2017 Jordan issues Science for Peace Declaration
On behalf of the coordinating organizations responsible for delivering the World Science Forum Jordan, the concluding Science for Peace Declaration issued at the Dead Sea represents a global call for action to science and society to build a future that promises greater equality, security and opportunity for all, and in which science plays an increasingly prominent role as an enabler of fair and sustainable development.

PETA science group promotes animal-free science at society of toxicology conference
The PETA International Science Consortium Ltd. is presenting two posters on animal-free methods for testing inhalation toxicity at the 56th annual Society of Toxicology (SOT) meeting March 12 to 16, 2017, in Baltimore, Maryland.

Citizen Science in the Digital Age: Rhetoric, Science and Public Engagement
James Wynn's timely investigation highlights scientific studies grounded in publicly gathered data and probes the rhetoric these studies employ.

Science/Science Careers' survey ranks top biotech, pharma, and biopharma employers
The Science and Science Careers' 2016 annual Top Employers Survey polled employees in the biotechnology, biopharmaceutical, pharmaceutical, and related industries to determine the 20 best employers in these industries as well as their driving characteristics.

Three natural science professors win TJ Park Science Fellowship
Professor Jung-Min Kee (Department of Chemistry, UNIST), Professor Kyudong Choi (Department of Mathematical Sciences, UNIST), and Professor Kwanpyo Kim (Department of Physics, UNIST) are the recipients of the Cheong-Am (TJ Park) Science Fellowship of the year 2016.

Read More: Science News and Science Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.