Successful ATAC-Seq From Snap-Frozen Equine Tissues.

Area of Science:

• Genomics
• Epigenetics
• Animal Science

Background:

• Transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) is vital for studying genome-wide chromatin accessibility.
• Many biobanks store snap-frozen tissues, limiting ATAC-seq applications.
• The equine Functional Annotation of Animal Genome (FAANG) project requires methods applicable to stored tissues.

Purpose of the Study:

• To evaluate the feasibility of using snap-frozen horse tissues for ATAC-seq.
• To compare ATAC-seq data from frozen tissues versus cryopreserved nuclei (CN) from fresh tissues.
• To establish guidelines for equine FAANG ATAC-seq experiments.

Main Methods:

• ATAC-seq was performed on nuclei isolated from snap-frozen horse liver and lamina tissues.
• Results were compared to ATAC-seq data from CN isolated at the time of tissue harvest.
• The number of accessible chromatin regions (peaks) was quantified for each condition.

Main Results:

• ATAC-seq successfully generated data from both frozen liver and lamina tissues.
• More accessible chromatin regions were identified using CN isolated at the time of tissue collection compared to frozen tissues.
• Liver tissue yielded 22,000-61,000 peaks, while lamina yielded 20,000-33,000 peaks.

Conclusions:

• Snap-frozen horse tissues are a viable alternative for ATAC-seq when fresh nuclei are unavailable.
• For optimal ATAC-seq results, especially in challenging tissues like lamina, isolating nuclei at the time of tissue collection is recommended.
• Tissue type and nuclei integrity are critical factors for successful ATAC-seq experimental design.