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BMC genomics2017; 18(1); 511; doi: 10.1186/s12864-017-3884-2

Identification of long non-coding RNA in the horse transcriptome.

Abstract: Efforts to resolve the transcribed sequences in the equine genome have focused on protein-coding RNA. The transcription of the intergenic regions, although detected via total RNA sequencing (RNA-seq), has yet to be characterized in the horse. The most recent equine transcriptome based on RNA-seq from several tissues was a prime opportunity to obtain a concurrent long non-coding RNA (lncRNA) database. This lncRNA database has a breadth of eight tissues and a depth of over 20 million reads for select tissues, providing the deepest and most expansive equine lncRNA database. Utilizing the intergenic reads and three categories of novel genes from a previously published equine transcriptome pipeline, we better describe these groups by annotating the lncRNA candidates. These lncRNA candidates were filtered using an approach adapted from human lncRNA annotation, which removes transcripts based on size, expression, protein-coding capability and distance to the start or stop of annotated protein-coding transcripts. Our equine lncRNA database has 20,800 transcripts that demonstrate characteristics unique to lncRNA including low expression, low exon diversity and low levels of sequence conservation. These candidate lncRNA will serve as a baseline lncRNA annotation and begin to describe the RNA-seq reads assigned to the intergenic space in the horse.
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Publication Date: 2017-07-04 PubMed ID: 28676104PubMed Central: PMC5496257DOI: 10.1186/s12864-017-3884-2Google Scholar: Lookup
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  • Research Support
  • N.I.H.
  • Extramural
  • Research Support
  • Non-U.S. Gov't

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 focused on identifying long non-coding RNA (lncRNA) within the horse transcriptome, utilizing RNA sequencing data from multiple tissues, leading to the creation of a comprehensive equine lncRNA database. This enriched database provides a baseline for future studies on the functional roles of lncRNA within the horse genome.

Background

  • The researchers noted that past research on the horse genome had primarily focused on protein-coding RNA. However, the transcription of intergenic regions had not been thoroughly analyzed in the horse, despite being detected via RNA sequencing (RNA-seq).
  • Typically, intergenic regions are areas of the genome located between the protein-coding genes that do not produce proteins themselves. However, these regions can produce non-coding RNA, such as lncRNA, which have various regulatory roles within the cell.

Methodology

  • To fill this gap, the researchers used a recent transcriptome dataset obtained from RNA sequencing of several horse tissues to generate a database of lncRNA. They focused on those that were previously studied, yet were categorized as “novel” due to their somewhat unidentified nature.
  • The researchers used an adapted methodology from human lncRNA annotation to filter out and identify genuine lncRNA candidates. This included removing transcripts based on their size, level of expression, protein-coding potential, and distance to the start or stop of existing protein-coding transcripts. As a result, the final equine lncRNA database had 20,800 transcripts.

Findings

  • The study found that the identified lncRNAs displayed unique characteristics such as low expression, limited exon diversity, and lower levels of sequence conservation compared to protein-coding genes. These characteristics are typical of lncRNAs and aligned with their potential function as regulatory molecules rather than protein-producing units.
  • This enriched lncRNA database provides not just a baseline for lncRNA annotation in the horse genome but also gives potential insight into the functional roles of these RNA molecules within the horse genome. This information allows for more precise description of the RNA-seq reads assigned to the intergenic regions in the horse genome.

Impact

  • The development of a comprehensive lncRNA database for the horse genome could pave the way for future research into the potential functions and significance of lncRNAs in equine biology, potentially leading to discoveries about genetic traits and disease susceptibilities in horses.

Cite This Article

APA
Scott EY, Mansour T, Bellone RR, Brown CT, Mienaltowski MJ, Penedo MC, Ross PJ, Valberg SJ, Murray JD, Finno CJ. (2017). Identification of long non-coding RNA in the horse transcriptome. BMC Genomics, 18(1), 511. https://doi.org/10.1186/s12864-017-3884-2

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 18
Issue: 1
Pages: 511
PII: 511

Researcher Affiliations

Scott, E Y
  • Department of Animal Science, University of California, Davis, USA.
Mansour, T
  • Department of Population Health and Reproduction, University of California, Davis, USA.
  • Department of Clinical Pathology, College of Medicine, Mansoura University, Mansoura, Egypt.
Bellone, R R
  • Department of Population Health and Reproduction, University of California, Davis, USA.
  • Veterinary Genetics Laboratory, University of California, Davis, USA.
Brown, C T
  • Department of Population Health and Reproduction, University of California, Davis, USA.
Mienaltowski, M J
  • Department of Animal Science, University of California, Davis, USA.
Penedo, M C
  • Veterinary Genetics Laboratory, University of California, Davis, USA.
Ross, P J
  • Department of Animal Science, University of California, Davis, USA.
Valberg, S J
  • Large Animal Clinical Sciences, Michigan State University, College of Veterinary Medicine, East Lansing, USA.
Murray, J D
  • Department of Animal Science, University of California, Davis, USA.
  • Department of Population Health and Reproduction, University of California, Davis, USA.
Finno, C J
  • Department of Population Health and Reproduction, University of California, Davis, USA. cjfinno@ucdavis.edu.

MeSH Terms

  • Animals
  • Databases, Genetic
  • Gene Expression Profiling
  • Horses / genetics
  • Horses / metabolism
  • Organ Specificity
  • RNA, Long Noncoding / genetics
  • Sequence Analysis, RNA
  • Transcriptome

Grant Funding

  • K01 OD015134 / NIH HHS
  • L40 TR001136 / NCATS NIH HHS

Conflict of Interest Statement

ETHICS APPROVAL AND CONSENT TO PARTICIPATE: The embryo, cerebellar and some of the spinal cord and brainstem tissues were collected with the approval from Animal Care and Use Committee at the University of California, Davis. The remaining of the brainstem and spinal cord and the muscle tissues were collected with approval from Animal Care and Use Committee at the University of Minnesota. The skin and retina tissues were collected with the approval from University of Saskatchewan Animal Care Committee. For client owned horses, written consent was obtained for contributions made to this research. CONSENT FOR PUBLICATION: All data is publically available and consent for use of all data is available. COMPETING INTERESTS: The authors declare that they have no competing interests. PUBLISHER’S NOTE: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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