Comparative Enhancer Map of Cattle Muscle Genome Annotated by ATAC-Seq

Area of Science:

• Genomics
• Molecular Biology
• Animal Science

Background:

• Interpreting genome-wide association study (GWAS) findings requires understanding regulatory elements.
• Cattle muscle genome annotation is crucial for identifying genetic mechanisms influencing traits.

Purpose of the Study:

• To annotate functional elements in the cattle muscle genome using ATAC-seq.
• To identify regulatory regions associated with muscle development and economically important traits.

Main Methods:

• Performed ATAC-seq on adult and embryo cattle muscle genomes.
• Identified differentially accessible regions (DARs), including promoters and enhancers.
• Validated enhancer activity using dual-luciferase reporter assays.

Main Results:

• Discovered 10,023 and 11,360 peaks in adult and embryo cattle, respectively.
• Identified 8,850 DARs, comprising 2,515 promoters and 4,319 putative enhancers.
• Validated enhancer activity for 12 out of 15 selected regions, linking them to genes like LCORL and FRMD8.
• Mapped 295 GWAS loci to 183 putative enhancers, including those associated with body weight and meat quality.

Conclusions:

• The study provides a valuable comparative enhancer map for the cattle muscle genome.
• Identified regulatory elements linked to crucial traits, facilitating genomic selection in beef cattle.
• Enhancer activity and GWAS associations highlight specific regions for further functional investigation.