Landscape of overlapping gene expression in the equine placenta

Pouya Dini, Jamie Norris, Hossam El Sheikh Ali, Shavahn C. Loux, Mariano Carossino, Alejandro Esteller-Vico, Ernest Bailey, Theodore Kalbfleisch, Peter Daels, Barry A. Ball

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

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.

Original languageEnglish
Article number503
JournalGenes
Volume10
Issue number7
DOIs
StatePublished - Jul 2019

Bibliographical note

Funding Information:
Funding: This work was funded by the Special Research Fund (BOF) at Ghent University, the Albert G. Clay Endowment, the Clay Visiting Scholar fellowship and the Paul Mellon Postdoctoral fellowship at the University of Kentucky.

Publisher Copyright:
© 2019 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

  • Chorioallantois
  • Different-strand overlapping transcripts
  • Equine
  • Overlap genes
  • Placenta
  • Pregnancy
  • Sense-antisense

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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