Genome-wide chromatin accessibility and selective signals of meat rabbits reveal key Cis-regulatory elements and variants during postnatal development of skeletal muscles in rabbits.

Background: The development of skeletal muscles is intricately modulated by multiple genetic factors and significantly impacts the economic value of meat rabbits. However, our knowledge of epigenetics in rabbit skeletal muscles remains largely unknown.

Results: In this study, we collected leg skeletal muscles of rabbits and performed assays for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) to detect open chromatin across three developmental stages: birth (D1), weaning (D35), and adulthood (D75). A total of 126,959 accessible chromatin regions (ACRs) were identified across samples, and a broad increase and decrease in chromatin accessibility were found from D1 to D35 and D35 to D75, respectively. Integrative analysis of chromatin accessibility and transcriptome data revealed ACRs that were nearly closed at D1 but highly accessible at D35 and D75 were significantly enriched in skeletal muscle development. Cis-regulation analysis further revealed that genes dominated by enhancers mainly play roles in the neuron development of rabbit skeletal muscles. Moreover, the detection of selection signals of meat rabbits and the footprinting analysis of transcription factor at open chromatin revealed that both base transversion (Chr13:12144967 A-> G) and the dynamics of chromatin accessibility at the PRDM1 binding site might regulate ZSWIM5 during the development of skeletal muscles in rabbits.

Conclusions: Our study provided a category of potential cis-regulatory elements for understanding the development of skeletal muscles at the tissue level and might facilitate potential insights into growth regulation in rabbits.