An organism's genome contains many sequence regions that perform diverse functions. Examples of such regions include genes, promoters, enhancers, and binding sites for regulatory proteins and RNAs. One of biology's most important open problems is how to take a genome sequence and predict which regions within it perform different functions. In recent years, deep learning has enabled dramatic advances across many fields by modeling complex relationships between entities. Several deep learning models have also proven successful in predicting the biological function of a portion of DNA from its sequence, revealing new insights into the complex rules underlying genome regulation and opening new possibilities in disease modeling and synthetic biology.