Landscape of Overlapping Gene Expression in the Equine Placenta.

Dini Dini,Bailey Bailey,Norris Norris,Carossino Carossino,Kalbfleisch Kalbfleisch,Daels Daels,Loux Loux,Esteller-Vico Esteller-Vico,Ball Ball,Ali Ali

doi:10.3390/genes10070503

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.

Highlights

Overlapping genes were initially thought to be only common in viruses, bacteria, mitochondria, and plasmids [1,2,3,4]
We further grouped the overlapping genes to four different categories: (A) Embedded (Antisense gene is fully embedded within the Sense gene); (B) embedded (Sense gene is fully embedded within the Antisense gene); (C) tail-to-tail (30 -region overlap); (D) head-to-head (50 -region overlap) (Figure 1)
* (A) embedded (Antisense gene is fully embedded within the Sense gene) and 100% of the length of the antisense genes are embedded in the sense gene; (B) embedded (Sense gene is fully embedded within the Antisense gene) and 100% of the length of the sense genes are embedded in the antisense gene; (C) tail-to-tail (30 -regions overlap); (D) head-to-head (50 -regions overlap)

Summary

Introduction

Overlapping genes were initially thought to be only common in viruses (both DNA and RNA viruses), bacteria, mitochondria, and plasmids [1,2,3,4]. Over the last few years, this view has changed with studies demonstrating the existence of many overlapping loci in human and murine genomes [5,6,7,8] Since both strands of DNA are used for transcription, two main types of overlap are possible: (1) The same-strand overlap in which the two genes involved are transcribed from the same strand and (2) the opposite-strand overlap (bi-directional transcription) in which the two genes are transcribed from different strands of the same locus [6,8]. The bidirectional transcription in the equine genome needs further characterization

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Conclusion