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Genes2019; 10(7); 503; doi: 10.3390/genes10070503

Landscape of Overlapping Gene Expression in the Equine Placenta.

Abstract: Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. These different-strand overlapping genes are potential sense-antisense (SAS) pairs, which might have regulatory effects on each other. In the present study, we identified the SAS loci in the equine genome using previously generated stranded, paired-end RNA sequencing data from the equine chorioallantois. We identified a total of 1261 overlapping loci. The ratio of the number of overlapping regions to chromosomal length was numerically higher on chromosome 11 followed by chromosomes 13 and 12. These results show that overlapping transcription is distributed throughout the equine genome, but that distributions differ for each chromosome. Next, we evaluated the expression patterns of SAS pairs during the course of gestation. The sense and antisense genes showed an overall positive correlation between the sense and antisense pairs. We further provide a list of SAS pairs with both positive and negative correlation in their expression patterns throughout gestation. This study characterizes the landscape of sense and antisense gene expression in the placenta for the first time and provides a resource that will enable researchers to elucidate the mechanisms of sense/antisense regulation during pregnancy.
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Publication Date: 2019-07-02 PubMed ID: 31269762PubMed Central: PMC6678446DOI: 10.3390/genes10070503Google Scholar: Lookup
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  • Journal Article
  • 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 study examines the prevalence and pattern of overlapping genes in the genome of a horse, using data from a previous gene sequencing study on the equine placenta. The researchers found such overlapping genes to be widespread throughout the equine genome, with implications for understanding gene regulation during pregnancy.

Background

  • The research paper explores the concept of overlapping genes in eukaryotic genomes, particularly those found in the genome of a horse. Such overlapping genes are classified as different-strand overlapping genes or potential sense-antisense (SAS) pairs, which may mutually regulate each other.

Methodology

  • The equine chorioallantois, a component of the placenta, served as the source of data for this study. The researchers used previously generated, strand-specific, paired-end RNA sequencing data to locate the SAS loci in the equine genome.
  • The primary focus of this study is on the identification of overlapping loci and the ratio of the number of overlapping regions to chromosomal length.

Findings

  • A total of 1261 overlapping loci were identified in the equine genome.
  • The distribution of overlapping transcription was found throughout the equine genome but varied for each chromosome. Chromosome 11 had the highest ratio of overlapping regions to chromosomal length, followed by chromosomes 13 and 12.
  • The researchers also studied the expression patterns of SAS pairs during gestation. The results indicated an overall positive correlation between the expression of sense and antisense pairs.

Significance of the study

  • The study presents a comprehensive characterization of sense/antisense gene expression in the placenta, a crucial aspect of gestation.
  • The results of this study will be beneficial for future research exploring the mechanisms of sense/antisense regulation during pregnancy, thus potentially contributing to a better understanding of mammalian reproduction and development.

Cite This Article

APA
Dini P, Norris J, Ali HE, Loux SC, Carossino M, Esteller-Vico A, Bailey E, Kalbfleisch T, Daels P, Ball BA. (2019). Landscape of Overlapping Gene Expression in the Equine Placenta. Genes (Basel), 10(7), 503. https://doi.org/10.3390/genes10070503

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 10
Issue: 7
PII: 503

Researcher Affiliations

Dini, Pouya
  • Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium.
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA.
Norris, Jamie
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA.
Ali, Hossam El-Sheikh
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA.
  • Theriogenology Department, Faculty of Veterinary Medicine, University of Mansoura, Mansoura City 35516, Egypt.
Loux, Shavahn C
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA.
Carossino, Mariano
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA.
  • Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA.
Esteller-Vico, Alejandro
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA.
  • Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA.
Bailey, Ernest
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA.
Kalbfleisch, Theodore
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA.
  • Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA.
Daels, Peter
  • Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium. peter.daels@ugent.be.
Ball, Barry A
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA. b.a.ball@uky.edu.

MeSH Terms

  • Animals
  • Female
  • Genes, Overlapping
  • Genetic Loci
  • Horses / genetics
  • Placenta / metabolism
  • Pregnancy
  • Transcriptome

Conflict of Interest Statement

The authors declare that they have no competing interests.

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Citations

This article has been cited 4 times.
  1. Orellana-Guerrero D, Uribe-Salazar JM, El-Sheikh Ali H, Scoggin KE, Ball B, Daels P, Finno CJ, Dini P. Dynamics of the Equine Placental DNA Methylome and Transcriptome from Mid- to Late Gestation. Int J Mol Sci 2023 Apr 11;24(8).
    doi: 10.3390/ijms24087084pubmed: 37108254google scholar: lookup
  2. Mei X, Xu L, Ren Y, Yu M, Kuang L, Li C, Zhang Y, Lu C, Wang Z, Guo Z, Xie X, Huang D, Zhang M. Transcriptome Comparison of Chorion-Attached and Non-chorion-attached Endometrium in Mid-gestation of Rabbit. Front Vet Sci 2022;9:838802.
    doi: 10.3389/fvets.2022.838802pubmed: 35372533google scholar: lookup
  3. Dini P, Kalbfleisch T, Uribe-Salazar JM, Carossino M, Ali HE, Loux SC, Esteller-Vico A, Norris JK, Anand L, Scoggin KE, Rodriguez Lopez CM, Breen J, Bailey E, Daels P, Ball BA. Parental bias in expression and interaction of genes in the equine placenta. Proc Natl Acad Sci U S A 2021 Apr 20;118(16).
    doi: 10.1073/pnas.2006474118pubmed: 33853939google scholar: lookup
  4. de la Fuente A, Scoggin C, Bradecamp E, Martin-Pelaez S, van Heule M, Troedsson M, Daels P, Meyers S, Dini P. Transcriptome Signature of Immature and In Vitro-Matured Equine Cumulus-Oocytes Complex. Int J Mol Sci 2023 Sep 6;24(18).
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