Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues

• Published in: Scientific reports Vol. 10; no. 1; p. 5230
• Main Authors: Halstead, M. M., Kern, C., Saelao, P., Chanthavixay, G., Wang, Y., Delany, M. E., Zhou, H., Ross, P. J.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 23.03.2020; Nature Publishing Group
• Subjects: 13; 38/23; 45/15; 631/114/2400; 631/1647/2210/2211; Animal tissues; Animals; Cell Nucleus - genetics; Chickens; Chromatin; Chromatin - metabolism; Chromatin Immunoprecipitation Sequencing - methods; Cryopreservation; Cryopreservation - methods; Deoxyribonuclease; Deoxyribonuclease I - metabolism; DNA, Intergenic; Gene expression; Genomes; High-Throughput Nucleotide Sequencing - methods; Humanities and Social Sciences; Livestock; Lung - cytology; Male; multidisciplinary; Muscle, Skeletal - cytology; Nuclei; Promoter Regions, Genetic; Ribonucleic acid; RNA; Science; Science (multidisciplinary); Spleen - cytology; Sucrose; Swine; Transcription factors; Transposase
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-61678-9

The use of Assay for Transposase-Accessible Chromatin (ATAC-seq) to profile chromatin accessibility has surged over the past years, but its applicability to tissues has been very limited. With the intent of preserving nuclear architecture during long-term storage, cryopreserved nuclei preparations from chicken lung were used to optimize ATAC-seq. Sequencing data were compared with existing DNase-seq, ChIP-seq, and RNA-seq data to evaluate library quality, ultimately resulting in a modified ATAC-seq method capable of generating high quality chromatin accessibility data from cryopreserved nuclei preparations. Using this method, nucleosome-free regions (NFR) identified in chicken lung overlapped half of DNase-I hypersensitive sites, coincided with active histone modifications, and specifically marked actively expressed genes. Notably, sequencing only the subnucleosomal fraction dramatically improved signal, while separation of subnucleosomal reads post-sequencing did not improve signal or peak calling. The broader applicability of this modified ATAC-seq technique was tested using cryopreserved nuclei preparations from pig tissues, resulting in NFR that were highly consistent among biological replicates. Furthermore, tissue-specific NFR were enriched for binding motifs of transcription factors related to tissue-specific functions, and marked genes functionally enriched for tissue-specific processes. Overall, these results provide insights into the optimization of ATAC-seq and a platform for profiling open chromatin in animal tissues.