Pig ATAC-Seq

Pigs are important domestic animals. They are closely related to humans and have similarities with humans in many aspects, such as physiological characteristics and pathological processes. They are commonly used as animal models in human biomedical research. With the development of biotechnology, especially gene editing technology and sequencing technology, pigs have become a virtual object for animal models of human diseases and xenotransplantation research.

Currently, epigenetic research in pigs is one of the priorities of scientists. As a new technique for epigenetic analysis, ATAC-seq can help scientists to analyze chromatin accessibility in pigs faster and easier by cleaving open nuclear chromatin regions at a specific Spatio-temporal location by the transposase, and then obtaining the regulatory sequences of all active transcripts in the genome at that specific spatio-temporal location.

At Lifeasible, we aim to apply ATAC-seq technology to pig development, pork quality, genetic improvement, breeding programs, etc. With our professional team, rich experience, and cutting-edge sequencing platform, we provide our customers with pig ATAC-Seq solutions to gain insight into more information related to pig chromatin.

Our Pig ATAC-Seq Service Content

• Using ATAC-seq to analyze potential mechanisms of muscle fiber development differences among different breeds of pigs

Muscle growth affects the diameter and area of muscle fibers, and muscle fibers are an important factor in determining pork quality. We determined and analyzed the chromatin accessibility of two pig species by the ATAC-seq technique. Data analysis revealed that ASNS, CARNS1, G0S2, PPP1R14C, and SH3BP5 are candidate genes affecting muscle development; TFAP4, MAX, NHLH1, FRX5, and TGIF1 are transcription factors that may affect muscle growth and development; classical signaling pathways such as Wnt and mTOR are also involved in regulating skeletal muscle development.

Figure 1. Data analysis after using ATAC-seq. (Miao, W, et al. 2021)

• Determination of cis-regulatory elements in the pip genome using ATAC-seq

Detailed information on cis-regulatory elements can be useful for genetic improvement or manipulation of pigs as a meat source and biomedical model. We used to sequence technologies, including ATAC-seq, to detect cis-regulatory elements in 12 different tissues from four pig breeds. Over 220,000 cis-regulatory elements were identified, providing a rich data resource for epigenetic studies in pigs.

Figure 2. Cis-regulatory elements identified in different tissues of different breeds of pigs. (Zhao, Y, et al. 2021)

• Probing the potential molecular mechanisms of regulatory variation in complex pig traits using ATAC-seq

The transposase-accessible chromatin landscape derived from ATAC-seq analysis is critical for elucidating tissue-specific regulatory sequences and regulatory variants of complex trait-associated motifs in pigs. Therefore, we used ATAC-seq to determine the genome-wide landscape of chromatin accessibility in 20 tissues in pigs and identified tissue-specific and conserved biologically functional regulatory elements.

Figure 3. Identification of chromatin accessibility by ATAC-seq in pigs. (Jiang, T, et al. 2022)

Technical Route of Pig ATAC-Seq

Sample Requirements

• Cells: > 2 × 10⁵
• Tissue: 50 mg/serving
• Take cells in a good growth state for trypsin digestion counting to ensure cell viability of 85% or more.
• Resuspend the cells in the cryopreservation solution and add 80-100,000 cells per cryopreservation tube. (Basic freezing solution recipe: 50% FBS + 40% complete medium + 10% DMSO)

Please note: Ensure sufficient dry ice when transporting samples to avoid temperature rise to destroy cell activity.

Bioinformatics Analysis Content

• Raw data collation, filtering, and quality assessment
• Reference genome annotation collation and statistics
• Reference sequence alignment analysis
• Peak calling
• Peak-associated gene GO annotation
• KEGG annotation of Peak-related genes
• Sample-to-sample differential Peak analysis
• Differential Peak-related gene GO enrichment analysis
• Differential Peak-related gene KEGG pathway enrichment analysis
• Nucleosome localization
• Genome-wide chromatin open mapping

Lifeasible's animal-oriented sequencing technology platform can provide customers with pig ATAC-seq services. Our scientific protocol design, strict quality control management, and professional analysis team can ensure that every step of the process will be completed with excellence. Please feel free to contact us for questions, inquiries, or collaboration.