Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts

Surag Nair, Daniel S. Kim, Jacob Perricone, Anshul Kundaje

Abstract: Genome-wide profiles of chromatin accessibility and gene expression in diverse cellular contexts are critical to decipher the dynamics of transcriptional regulation. Recently, convolutional neural networks have been used to learn predictive cis-regulatory DNA sequence models of context-specific chromatin accessibility landscapes. However, these context-specific regulatory sequence models cannot generalize predictions across cell types.