Analysis of unannotated equine transcripts identified by mRNA sequencing.
Abstract: Sequencing of equine mRNA (RNA-seq) identified 428 putative transcripts which do not map to any previously annotated or predicted horse genes. Most of these encode the equine homologs of known protein-coding genes described in other species, yet the potential exists to identify novel and perhaps equine-specific gene structures. A set of 36 transcripts were prioritized for further study by filtering for levels of expression (depth of RNA-seq read coverage), distance from annotated features in the equine genome, the number of putative exons, and patterns of gene expression between tissues. From these, four were selected for further investigation based on predicted open reading frames of greater than or equal to 50 amino acids and lack of detectable homology to known genes across species. Sanger sequencing of RT-PCR amplicons from additional equine samples confirmed expression and structural annotation of each transcript. Functional predictions were made by conserved domain searches. A single transcript, expressed in the cerebellum, contains a putative kruppel-associated box (KRAB) domain, suggesting a potential function associated with zinc finger proteins and transcriptional regulation. Overall levels of conserved synteny and sequence conservation across a 1MB region surrounding each transcript were approximately 73% compared to the human, canine, and bovine genomes; however, the four loci display some areas of low conservation and sequence inversion in regions that immediately flank these previously unannotated equine transcripts. Taken together, the evidence suggests that these four transcripts are likely to be equine-specific.
Publication Date: 2013-07-29 PubMed ID: 23922931PubMed Central: PMC3726457DOI: 10.1371/journal.pone.0070125Google Scholar: Lookup
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- Journal Article
- Research Support
- N.I.H.
- Extramural
- Research Support
- Non-U.S. Gov't
Summary
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The research identified 428 potentially new horse gene transcripts based on the sequencing of equine mRNA. The researchers prioritized a select group of these potential genes for further investigation, based primarily on their expression levels and sequence structure. After further investigation, the team suspects that these four transcripts might be unique to horses.
Objective of the Research
- The aim of this study was to analyze unannotated equine transcripts that were identified through mRNA sequencing. 428 such potential transcripts were identified, and out of these, four were selected for further investigation based on their predicted open reading frames and lack of detectable homology to known genes. The goal was to broaden the understanding of equine genomic uniqueness and potentially discover equine-specific genes.
Methodology
- Through mRNA sequencing, researchers identified 428 putative transcripts that don’t match any previously known or predicted horse genes. These putative transcripts could possibly be encoding for equine homologs of known protein-coding genes from other species.
- A set of 36 of these transcripts were prioritized for further research. The selection criteria for these 36 was based on their levels of expression, distance from previously annotated features in the equine genome, the number of putative exons, and differential gene expression across tissues.
- Out of the prioritized 36, four transcripts were chosen for deeper investigation as they had predicted open reading frames of greater than or equal to 50 amino acids and showed no detectable similarity to known genes across species.
- Sanger sequencing was performed on RT-PCR amplicons from additional horse samples to confirm the expression and structural annotation of each of the four transcripts.
Findings
- One of the analyzed transcripts, expressed in the cerebellum, was found to contain a putative kruppel-associated box (KRAB) domain, suggesting a potential function related to zinc finger proteins and transcriptional regulation.
- Upon comparing the surrounding 1MB region of each transcript with the human, canine, and bovine genomes, approximately 73% of conserved synteny and sequence conservation was found. Despite the high genetic similarity, the researchers did note areas of low conservation and sequence inversion in regions directly surrounding these previously unannotated equine transcripts.
- The results indicate these four transcripts are likely to be equine-specific as a result of the sequence inversion and regions of low conservation around their sequences.
Cite This Article
APA
Coleman SJ, Zeng Z, Hestand MS, Liu J, Macleod JN.
(2013).
Analysis of unannotated equine transcripts identified by mRNA sequencing.
PLoS One, 8(7), e70125.
https://doi.org/10.1371/journal.pone.0070125 Publication
Researcher Affiliations
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America.
MeSH Terms
- Animals
- Cattle
- Computational Biology / methods
- Dogs
- Evolution, Molecular
- Gene Expression Profiling
- Horses
- Humans
- Molecular Sequence Annotation
- RNA, Messenger / chemistry
- RNA, Messenger / genetics
- Reproducibility of Results
- Sequence Analysis, RNA
Grant Funding
- P20 RR016481 / NCRR NIH HHS
- R01 HG006272 / NHGRI NIH HHS
- KY-INBRE P20 RR16481 / NCRR NIH HHS
- P20 RR16481 / NCRR NIH HHS
Conflict of Interest Statement
The authors have declared that no competing interests exist.
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Citations
This article has been cited 8 times.- Premont A, Saadeh K, Edling C, Lewis R, Marr CM, Jeevaratnam K. Cardiac ion channel expression in the equine model - In-silico prediction utilising RNA sequencing data from mixed tissue samples.. Physiol Rep 2022 Jul;10(14):e15273.
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