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

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 f...

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Bibliographic Details
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
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	2045-2322 2045-2322
DOI:	10.1038/s41598-020-61678-9