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Home / Equine Research Bank / Front Genet / Successful ATAC-Seq From Snap-Frozen Equine Tissues.
Frontiers in genetics2021; 12; 641788; doi: 10.3389/fgene.2021.641788

Successful ATAC-Seq From Snap-Frozen Equine Tissues.

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.
Copyright © 2021 Peng, Bellone, Petersen, Kalbfleisch and Finno.
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Publication Date: 2021-06-16 PubMed ID: 34220931PubMed Central: PMC8242358DOI: 10.3389/fgene.2021.641788Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research article examines the effectiveness of using snap-frozen equine tissues in ATAC-Seq processes which investigate genome-wide chromatin accessibility in isolated nuclei. The results illustrate that while it is possible and acceptable to use frozen tissues, extracting nuclei at the time of collection can give optimal results especially for tougher tissue types like lamina.

Understanding ATAC-Seq and Snap-Frozen Equine Tissues

  • ATAC-seq is a method used to analyse chromatin accessibility throughout the genome. It examines the areas of the genome that are open and available for transcription, thus contributing to understanding how genes are regulated.
  • This research focuses on using snap-frozen equine tissues for ATAC-seq. Many biobanks contain such frozen tissue samples, making them practical for this type of sequencing.
  • The research was a part of the FAANG project, an international collaboration focused on annotating animal genomes.

Significance of Tissue Type

  • The scientists explored the impact of tissue type by comparing the results of ATAC-seq from nuclei isolated from frozen tissue to freshly isolated nuclei, using liver and lamina tissues from horses.
  • Liver is a homogenous and densely cellular tissue, while lamina is relatively acellular and specific to horses. This comparison helped determine how different tissue types affect ATAC-Seq results.

Findings of the Study

  • The researchers identified up to 33,000 accessible chromatin regions in lamina and up to 61,000 in liver.
  • It was found that more peaks were identified using freshly isolated nuclei at the time of tissue collection than with nuclei from frozen tissues.
  • Despite this, the findings suggest that using frozen tissues is an acceptable alternative when fresh tissues are unavailable. However, for more challenging tissue types such as lamina, extracting nuclei at the time of collection is preferred for optimal results.

Implications of the Research

  • The outcome of this research provides valuable insights for the equine FAANG project and similar genomic studies.
  • Knowing that frozen tissues can be used effectively in ATAC-seq expands the potential sources of material for such studies, particularly when fresh tissues may be difficult to obtain.
  • Additionally, it highlights the importance of considering tissue type and accessibility to intact nuclei when designing ATAC-seq experiments.

Cite This Article

APA
Peng S, Bellone R, Petersen JL, Kalbfleisch TS, Finno CJ. (2021). Successful ATAC-Seq From Snap-Frozen Equine Tissues. Front Genet, 12, 641788. https://doi.org/10.3389/fgene.2021.641788

Publication

Frontiers in genetics
ISSN: 1664-8021
NlmUniqueID: 101560621
Country: Switzerland
Language: English
Volume: 12
Pages: 641788
PII: 641788

Researcher Affiliations

Peng, Sichong
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
Bellone, Rebecca
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
Petersen, Jessica L
  • Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States.
Kalbfleisch, Theodore S
  • Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States.
Finno, Carrie J
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.

Conflict of Interest Statement

The cost of library preparation and sequencing was partially covered by two core laboratories as part of collaboration to optimize ATAC-seq protocol using horse tissues.

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Citations

This article has been cited 8 times.
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