A New Genetic Tool for Predicting Regulatory Sequences

 

    A project conducted by members of the UC San Diego Department of Medicine resulted in the creation of EUGENe, a tool designed to assist in the prediction of regulatory sequences. The team lists a lack of deep-learning methods for regulatory genetics that follow the FAIR(findable, accessible, interoperable, reusable) principle, and created EUGENe to fill that gap in technology.

    The team states that EUGENe is  "a simple, flexible and extensible interface for streamlining and customizing end-to-end deep-learning sequence analyses." The team discusses the lack of software that can effectively tackle the problems faced in deep-learning related genetics and goes into detail about the failures that each of the current major packages has in regards to a comprehensive package that can handle an end-to-end workflow while integrating with other available packages.

Article on EUGENe

Klie, A., Laub, D., Talwar, J.V. et al. Predictive analyses of regulatory sequences with EUGENe. Nat Comput Sci 3, 946–956 (2023). https://doi.org/10.1038/s43588-023-00544-w

Article on Janggu, a major software package that handles deep-learning in genomics

Kopp, W., Monti, R., Tamburrini, A. et al. Deep learning for genomics using Janggu. Nat Commun 11, 3488 (2020). https://doi.org/10.1038/s41467-020-17155-y

USDA Regulation of CRISPR-edited Crops

The USDA or the United States Department of Agriculture has restrictions on GMO crops that contain artificially inserted genes from other species. However, the USDA recently released a statement that they will not regulate plants that have been modified using genome editing. This includes the somewhat recent technology of CRISPR genome editing. CRISPR or clustered regularly interspaced short palindromic repeats, these can be programmed to target specific stretches of genetic code and edit it at precise locations. The USDA did clarify that they will not oversee the use of these plants, as long as they could have been developed using traditional breeding methods, such as cross breeding. The only difference should be the speed at which the trait is introduced. It is unclear whether these special gene-edited plants will require special labeling once they hit the shelves; however, it seems that if it is a gene introduced that could naturally have been breed in then it would not.
This is shocking to me, not because the crops would pose any risk to human health but because governments love to regulate things. I don't really see the downside of regulating these crops but I suppose that if the genes could been introduced naturally then it makes sense that they would not be regulated. Very interesting though, I think there will be more backlash from this once these crops get closer to being on the market. I don't think a person without a background in science would really understand what they are doing so they probably will at least want the foods labeled.

https://www.the-scientist.com/?articles.view/articleNo/52209/title/USDA-Will-Not-Regulate-CRISPR-Edited-Crops/
https://www.broadinstitute.org/what-broad/areas-focus/project-spotlight/questions-and-answers-about-crispr