Chromatin Accessibility in Porcine Liver, Spleen and Circulating Immune Cells

Chromatin accessibility is an essential form of control for all classes of cis-regulatory elements such as binding sites for transcription factors, promoters, enhancers/silencers and insulators. DNase-seq is commonly used to determine chromatin accessibility (e.g. in the ENCODE projects). Recently, the assay for transposase-accessible chromatin sequencing (ATAC-seq), which is based on direct in vitro transposition of sequencing adaptors into native chromatin, was introduced as an alternative to DNase-seq. ATAC-seq is able to interrogate an entire genome and provide information about chromatin accessibility, nucleosome occupancy and transcription factor occupancy. It has advantages over DNase-seq because it requires fewer cells, and has a fast and simple DNA fragmentation and library preparation protocol.

As part of the Fr-AgENCODE project within the FAANG consortium we are optimizing conditions for conducting ATAC-seq on primary cells and tissues. We collected liver, spleen, CD4+ and CD8+ T cells from pigs, goats and chickens. In vitro transposition was carried out on fresh samples at the sampling site after cell dissociation (liver, spleen) or on CD4+ and CD8+ T-cells. We completed preparation and quality control of test libraries from pig CD3+CD4+, CD3+CD8+, T-cells, liver and spleen, plus a control library from the GM12878 human cell line; sequencing is currently in progress. We are concurrently developing a pipeline for data QC and analysis.

This is the first time that ATAC-seq has been applied to pig primary tissues/ cells and the data generated will be used to optimize sample collection, library preparation and data analysis protocols for broader application of ATAC-seq within FAANG.