Welcome to Mouse Encode Project at Ren Lab!

As the most widely used mammalian model organism, mice play a critical role in biomedical research for mechanistic study of human development and diseases. Today, functional sequences in the mouse genome are still poorly annotated, lagging significantly behind that of several other model organisms. We report here a map of nearly 300,000 murine cis-regulatory sequences, representing active promoters, enhancers and CTCF binding sites experimentally determined from a diverse set of 19 tissues and cell types. This map provides functional annotation to nearly 11% of the mouse genome, and over 70% of conserved, non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we demonstrate that cis-regulatory sequences are organized into domains of coordinately regulated enhancers and promoters. Our results provide a resource for the annotation of functional elements in the mammalian genome, and study of regulatory mechanisms for tissue-specific gene expression.