Landscape of Overlapping Gene Expression in The Equine Placenta
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...
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doaj-f370cbb3f6e04b7f8142e1c0e76f22c62020-11-25T01:42:51ZengMDPI AGGenes2073-44252019-07-0110750310.3390/genes10070503genes10070503Landscape of Overlapping Gene Expression in The Equine PlacentaPouya Dini0Jamie Norris1Hossam El-Sheikh Ali2Shavahn C. Loux3Mariano Carossino4Alejandro Esteller-Vico5Ernest Bailey6Theodore Kalbfleisch7Peter Daels8Barry A. Ball9Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, BelgiumGluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USAGluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USAGluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USAGluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USAGluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USAGluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USAGluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USAFaculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, BelgiumGluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USAIncreasing 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.https://www.mdpi.com/2073-4425/10/7/503overlap genessense-antisensedifferent-strand overlapping transcriptspregnancyplacentaequinechorioallantois |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
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 |
spellingShingle |
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 Landscape of Overlapping Gene Expression in The Equine Placenta Genes overlap genes sense-antisense different-strand overlapping transcripts pregnancy placenta equine chorioallantois |
author_facet |
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 |
author_sort |
Pouya Dini |
title |
Landscape of Overlapping Gene Expression in The Equine Placenta |
title_short |
Landscape of Overlapping Gene Expression in The Equine Placenta |
title_full |
Landscape of Overlapping Gene Expression in The Equine Placenta |
title_fullStr |
Landscape of Overlapping Gene Expression in The Equine Placenta |
title_full_unstemmed |
Landscape of Overlapping Gene Expression in The Equine Placenta |
title_sort |
landscape of overlapping gene expression in the equine placenta |
publisher |
MDPI AG |
series |
Genes |
issn |
2073-4425 |
publishDate |
2019-07-01 |
description |
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. |
topic |
overlap genes sense-antisense different-strand overlapping transcripts pregnancy placenta equine chorioallantois |
url |
https://www.mdpi.com/2073-4425/10/7/503 |
work_keys_str_mv |
AT pouyadini landscapeofoverlappinggeneexpressionintheequineplacenta AT jamienorris landscapeofoverlappinggeneexpressionintheequineplacenta AT hossamelsheikhali landscapeofoverlappinggeneexpressionintheequineplacenta AT shavahncloux landscapeofoverlappinggeneexpressionintheequineplacenta AT marianocarossino landscapeofoverlappinggeneexpressionintheequineplacenta AT alejandroestellervico landscapeofoverlappinggeneexpressionintheequineplacenta AT ernestbailey landscapeofoverlappinggeneexpressionintheequineplacenta AT theodorekalbfleisch landscapeofoverlappinggeneexpressionintheequineplacenta AT peterdaels landscapeofoverlappinggeneexpressionintheequineplacenta AT barryaball landscapeofoverlappinggeneexpressionintheequineplacenta |
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