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Non-coding RNA2020; 6(3); 32; doi: 10.3390/ncrna6030032

Comparison of Poly-A+ Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq.

Abstract: Long non-coding RNAs (lncRNAs) are untranslated regulatory transcripts longer than 200 nucleotides that can play a role in transcriptional, post-translational, and epigenetic regulation. Traditionally, RNA-sequencing (RNA-seq) libraries have been created by isolating transcriptomic RNA via poly-A selection. In the past 10 years, methods to perform ribosomal RNA (rRNA) depletion of total RNA have been developed as an alternative, aiming for better coverage of whole transcriptomic RNA, both polyadenylated and non-polyadenylated transcripts. The purpose of this study was to determine which library preparation method is optimal for lncRNA investigations in the horse. Using liver and cerebral parietal lobe tissues from two healthy Thoroughbred mares, RNA-seq libraries were prepared using standard poly-A selection and rRNA-depletion methods. Averaging the two biologic replicates, poly-A selection yielded 327 and 773 more unique lncRNA transcripts for liver and parietal lobe, respectively. More lncRNA were found to be unique to poly-A selected libraries, and rRNA-depletion identified small nucleolar RNA (snoRNA) to have a higher relative expression than in the poly-A selected libraries. Overall, poly-A selection provides a more thorough identification of total lncRNA in equine tissues while rRNA-depletion may allow for easier detection of snoRNAs.
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Publication Date: 2020-08-21 PubMed ID: 32825772PubMed Central: PMC7549351DOI: 10.3390/ncrna6030032Google 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.

The research article focuses on which RNA library preparation method is most effective for the study of long non-coding RNAs in horse tissues. Two methods, poly-A selection and rRNA depletion, were compared and it was found that the poly-A selection method provided a more comprehensive identification of long non-coding RNAs.

Background

  • Long non-coding RNAs (lncRNAs) are regulatory transcripts that do not code for proteins but play significant roles in various biological processes such as transcriptional, post-translational, and epigenetic regulation.
  • The detection and identification of lncRNAs is critical for understanding many biological and physiological processes.
  • Traditionally, libraries for RNA-sequencing studies have been created by isolating transcriptomic RNA through a method known as poly-A selection. More recently, a technique to deplete ribosomal RNA (rRNA) from total RNA has been developed, aiming to give improved coverage of the entire transcriptomic RNA, including both polyadenylated and non-polyadenylated transcripts.

Objective and Methods

  • The aim of the study was to find out which library preparation method – poly-A selection or rRNA depletion – is more suitable for studying lncRNAs in the horse.
  • To do this, the researchers compared these two methods by analyzing liver and cerebral parietal lobe tissues from two healthy Thoroughbred mares.

Findings

  • When averaging the results of the two biological replicates, it was found that poly-A selection yielded 327 and 773 more unique lncRNA transcripts for liver and parietal lobe, respectively.
  • The study discovered that more lncRNAs were unique to libraries prepared using poly-A selection. However, despite this, rRNA depletion identified a higher relative expression of small nucleolar RNAs (snoRNAs) in comparison to the poly-A selection method.

Conclusion

  • The research concluded that poly-A selection provides a more thorough identification of total long non-coding RNAs in horse tissues.
  • However, it was also noted that the rRNA depletion method may allow for easier detection of snoRNAs.

Cite This Article

APA
Dahlgren AR, Scott EY, Mansour T, Hales EN, Ross PJ, Kalbfleisch TS, MacLeod JN, Petersen JL, Bellone RR, Finno CJ. (2020). Comparison of Poly-A+ Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq. Noncoding RNA, 6(3), 32. https://doi.org/10.3390/ncrna6030032

Publication

Non-coding RNA
ISSN: 2311-553X
NlmUniqueID: 101652294
Country: Switzerland
Language: English
Volume: 6
Issue: 3
PII: 32

Researcher Affiliations

Dahlgren, Anna R
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.
Scott, Erica Y
  • Department of Animal Science, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA 95616, USA.
Mansour, Tamer
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.
Hales, Erin N
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.
Ross, Pablo J
  • Department of Animal Science, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA 95616, USA.
Kalbfleisch, Theodore S
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA.
MacLeod, James N
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA.
Petersen, Jessica L
  • Department of Animal Science, University of Nebraska Lincoln, Lincoln, NE 68583, USA.
Bellone, Rebecca R
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.
Finno, Carrie J
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.

Grant Funding

  • N/A / Grayson Jockey Club Foundation
  • NRSP-8 Species Coordinator Funds / U.S. Department of Agriculture
  • N/A / UC Davis Center for Equine Health
  • 20143842021796 (Hales) / U.S. Department of Agriculture
  • L40 TR001136 (Finno) / NIH HHS

Conflict of Interest Statement

The authors declare no conflict of interest.

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Citations

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