Scientists at La Jolla Institute for Immunology (LJI) have developed a new computational method for linking molecular marks on our DNA to gene activity.
Jun 4 2024La Jolla Institute for Immunology Scientists at La Jolla Institute for Immunology have developed a new computational method for linking molecular marks on our DNA to gene activity. Their work may help researchers connect genes to the molecular "switches" that turn them on or off.
Ay and Rao are working to pinpoint regions of the genome that contain molecular enhancers, or "switches," which fine tune the levels of gene expression and determine when and where genes will be on or off. This work requires researchers to develop computational tools that can harness complex genomic data and find which enhancers are connected to which genes.
The neural network goes to work The researchers trained new neural networks that learn how the presence of an important DNA modification called 5hmC, either near the gene or far away from it, is related to gene expression activity. This attachment of a hydroxymethyl group to cytosine has been associated with enhancer activity.
This 5hmC distribution controlled the expression of different gene sets in these different types of cells. The researchers had found that 5hmC attaches to regions of the genomes that work as enhancers-;the same regions that help switch gene expression on and off-;as well as to the genes themselves. These differences in active genes and enhancers are what distinguishes a liver cell from cells in the lung or neurons in the brain.
The new research method allows a simpler connection to be made between genes and enhancers than was possible with earlier methods. "What is exciting is that some of these distant enhancers are novel regulatory elements that have not been discovered before," says Ay.
Research Blood Brain Cancer Cell Cytosine DNA Gene Gene Expression Genome Genomic Immunology Liver Machine Learning Neurons Ph
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