Genome-Wide Annotation of Promoter-Enhancer Interactions via Chromatin Loops in the Hybrid Rat Diversity Panel
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The three-dimensional organization of the genome is critical for gene regulation, in part by facilitating interactions between promoters and distal regulatory elements. However, high-resolution maps of chromatin loops in the rat are not yet well-established. In this study, we generated a genome-wide annotation of chromatin loops in the frontal cortex of ten inbred rat strains from the Hybrid Rat Diversity Panel. Using Hi-C data processed through the Juicer pipeline and HiCCUPS, we identified an average of 5,899 loops per sample, with detection rates influenced by both sequencing depth and resolution. By integrating these data with annotations for CTCF binding sites, transcription start sites, and promoters, we identified 23,640 unique, high-confidence regulatory loops. These loops are distributed throughout the genome and provide a foundational resource for investigating gene regulation and the genetic architecture of complex traits in rat models.
