Predicting the impact of sequence motifs on gene regulation using single-cell data

• Main Author: Hepkema J.
• Other Authors: Mahidol University
• Format: Article
• Published: 2023
• Subjects: Agricultural and Biological Sciences
• Online Access: https://repository.li.mahidol.ac.th/handle/123456789/88815

The binding of transcription factors at proximal promoters and distal enhancers is central to gene regulation. Identifying regulatory motifs and quantifying their impact on expression remains challenging. Using a convolutional neural network trained on single-cell data, we infer putative regulatory motifs and cell type-specific importance. Our model, scover, explains 29% of the variance in gene expression in multiple mouse tissues. Applying scover to distal enhancers identified using scATAC-seq from the developing human brain, we identify cell type-specific motif activities in distal enhancers. Scover can identify regulatory motifs and their importance from single-cell data where all parameters and outputs are easily interpretable.