Successful ATAC-Seq from Snap-Frozen Equine Tissues

Authors

Sichong Peng, University of California, Davis
Rebecca Bellone, University of California, Davis
Jessica L. Petersen, University of Nebraska-Lincoln
Theodore S. Kalbfleisch, University of KentuckyFollow
Carrie J. Finno, University of California, Davis

Abstract

An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has become an increasingly popular method to assess genome-wide chromatin accessibility in isolated nuclei from fresh tissues. However, many biobanks contain only snap-frozen tissue samples. While ATAC-seq has been applied to frozen brain tissues in human, its applicability in a wide variety of tissues in horse remains unclear. The Functional Annotation of Animal Genome (FAANG) project is an international collaboration aimed to provide high quality functional annotation of animal genomes. The equine FAANG initiative has generated a biobank of over 80 tissues from two reference female animals and experiments to begin to characterize tissue specificity of genome function for prioritized tissues have been performed. Due to the logistics of tissue collection and storage, extracting nuclei from a large number of tissues for ATAC-seq at the time of collection is not always practical. To assess the feasibility of using stored frozen tissues for ATAC-seq and to provide a guideline for the equine FAANG project, we compared ATAC-seq results from nuclei isolated from frozen tissue to cryopreserved nuclei (CN) isolated at the time of tissue harvest in liver, a highly cellular homogenous tissue, and lamina, a relatively acellular tissue unique to the horse. We identified 20,000–33,000 accessible chromatin regions in lamina and 22–61,000 in liver, with consistently more peaks identified using CN isolated at time of tissue collection. Our results suggest that frozen tissues are an acceptable substitute when CN are not available. For more challenging tissues such as lamina, nuclei extraction at the time of tissue collection is still preferred for optimal results. Therefore, tissue type and accessibility to intact nuclei should be considered when designing ATAC-seq experiments.

Document Type

Article

Publication Date

6-16-2021

Notes/Citation Information

Published in Frontiers in Genetics, v. 12, article 641788.

© 2021 Peng, Bellone, Petersen, Kalbfleisch and Finno

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

Digital Object Identifier (DOI)

https://doi.org/10.3389/fgene.2021.641788

Funding Information

Funding was provided by the Grayson Jockey Club Foundation, USDA NRSP-8, and the UC Davis Center for Equine Health. Funding Support for CF was provided by the National Institutes of Health (NIH) (L40 TR001136). None of the funding agencies had any role in the design of the study, analysis, interpretation of the data, or writing of the manuscript. Salary support for SP was provided by the Ann T. Bowling Fellowship at the UC Davis Veterinary Genetics Laboratory.

Related Content

ATAC-seq data used in this study are available from the European Nucleotide Archive under the accession PRJEB41317. RNA-seq data from the liver and lamina tissues of the same two animals used in this study can be found from the European Nucleotide Archive under the accession PRJEB26787.

Repository Citation

Peng, Sichong; Bellone, Rebecca; Petersen, Jessica L.; Kalbfleisch, Theodore S.; and Finno, Carrie J., "Successful ATAC-Seq from Snap-Frozen Equine Tissues" (2021). Veterinary Science Faculty Publications. 54.
https://uknowledge.uky.edu/gluck_facpub/54