Comparison of Poly-A<sup>+</sup> Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq
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<...
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MDPI AG
2020-08-01
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| Series: | Non-Coding RNA |
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| Online Access: | https://www.mdpi.com/2311-553X/6/3/32 |
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| author | Anna R. Dahlgren Erica Y. Scott Tamer Mansour Erin N. Hales Pablo J. Ross Theodore S. Kalbfleisch James N. MacLeod Jessica L. Petersen Rebecca R. Bellone Carrie J. Finno |
| author_facet | Anna R. Dahlgren Erica Y. Scott Tamer Mansour Erin N. Hales Pablo J. Ross Theodore S. Kalbfleisch James N. MacLeod Jessica L. Petersen Rebecca R. Bellone Carrie J. Finno |
| author_sort | Anna R. Dahlgren |
| collection | DOAJ |
| description | 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<sup>+</sup> 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<sup>+</sup> selection and rRNA-depletion methods. Averaging the two biologic replicates, poly-A<sup>+</sup> 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<sup>+</sup> selected libraries, and rRNA-depletion identified small nucleolar RNA (snoRNA) to have a higher relative expression than in the poly-A<sup>+</sup> selected libraries. Overall, poly-A<sup>+</sup> selection provides a more thorough identification of total lncRNA in equine tissues while rRNA-depletion may allow for easier detection of snoRNAs. |
| first_indexed | 2024-03-10T17:00:50Z |
| format | Article |
| id | doaj.art-72db4a549f764aac83aa2139fc04b8b4 |
| institution | Directory Open Access Journal |
| issn | 2311-553X |
| language | English |
| last_indexed | 2024-03-10T17:00:50Z |
| publishDate | 2020-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Non-Coding RNA |
| spelling | doaj.art-72db4a549f764aac83aa2139fc04b8b42023-11-20T10:57:32ZengMDPI AGNon-Coding RNA2311-553X2020-08-01633210.3390/ncrna6030032Comparison of Poly-A<sup>+</sup> Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seqAnna R. Dahlgren0Erica Y. Scott1Tamer Mansour2Erin N. Hales3Pablo J. Ross4Theodore S. Kalbfleisch5James N. MacLeod6Jessica L. Petersen7Rebecca R. Bellone8Carrie J. Finno9Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USADepartment of Animal Science, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA 95616, USADepartment of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USADepartment of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USADepartment of Animal Science, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA 95616, USAGluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USAGluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USADepartment of Animal Science, University of Nebraska Lincoln, Lincoln, NE 68583, USADepartment of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USADepartment of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USALong 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<sup>+</sup> 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<sup>+</sup> selection and rRNA-depletion methods. Averaging the two biologic replicates, poly-A<sup>+</sup> 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<sup>+</sup> selected libraries, and rRNA-depletion identified small nucleolar RNA (snoRNA) to have a higher relative expression than in the poly-A<sup>+</sup> selected libraries. Overall, poly-A<sup>+</sup> selection provides a more thorough identification of total lncRNA in equine tissues while rRNA-depletion may allow for easier detection of snoRNAs.https://www.mdpi.com/2311-553X/6/3/32annotationtranscriptomeregulatoryhorse |
| spellingShingle | Anna R. Dahlgren Erica Y. Scott Tamer Mansour Erin N. Hales Pablo J. Ross Theodore S. Kalbfleisch James N. MacLeod Jessica L. Petersen Rebecca R. Bellone Carrie J. Finno Comparison of Poly-A<sup>+</sup> Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq Non-Coding RNA annotation transcriptome regulatory horse |
| title | Comparison of Poly-A<sup>+</sup> Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq |
| title_full | Comparison of Poly-A<sup>+</sup> Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq |
| title_fullStr | Comparison of Poly-A<sup>+</sup> Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq |
| title_full_unstemmed | Comparison of Poly-A<sup>+</sup> Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq |
| title_short | Comparison of Poly-A<sup>+</sup> Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq |
| title_sort | comparison of poly a sup sup selection and rrna depletion in detection of lncrna in two equine tissues using rna seq |
| topic | annotation transcriptome regulatory horse |
| url | https://www.mdpi.com/2311-553X/6/3/32 |
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