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Parental bias in expression and interaction of genes in the equine placenta

Pouya Dini, Theodore Kalbfleisch, José M. Uribe-Salazar, Mariano Carossino, Hossam El-Sheikh Ali, Shavahn C. Loux, Alejandro Esteller-Vico, Jamie K. Norris, Lakshay Anand, Kirsten E. Scoggin, et al.
(2021) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 118(16).
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Abstract
Most autosomal genes in the placenta show a biallelic expression pattern. However, some genes exhibit allele-specific transcription depending on the parental origin of the chromosomes on which the copy of the gene resides. Parentally expressed genes are involved in the reciprocal interaction between maternal and paternal genes, coordinating the allocation of resources between fetus and mother. One of the main challenges of studying parental-specific allelic expression (allele-specific expression [ASE]) in the placenta is the maternal cellular remnant at the fetomaternal interface. Horses (Equus caballus) have an epitheliochorial placenta in which both the endometrial epithelium and the epithelium of the chorionic villi are juxtaposed with minimal extension into the uterine mucosa, yet there is no information available on the allelic gene expression of equine chorioallantois (CA). In the current study, we present a dataset of 1,336 genes showing ASE in the equine CA (https://pouya-dini.github.io/equine-gene-db/) along with a work-flow for analyzing ASE genes. We further identified 254 potentially imprinted genes among the parentally expressed genes in the equine CA and evaluated the expression pattern of these genes throughout gestation. Our gene ontology analysis implies that maternally expressed genes tend to decrease the length of gestation, while paternally expressed genes extend the length of gestation. This study provides fundamental information regarding parental gene expression during equine pregnancy, a species with a negligible amount of maternal cellular remnant in its placenta. This information will provide the basis for a better understanding of the role of parental gene expression in the placenta during gestation.
Keywords
allele-specific expression, parental gene expression, monoallelic gene expression, placenta, equine, GENOME-WIDE ANALYSIS, DNA METHYLATION, IMPRINTED GENE, ANTISENSE TRANSCRIPTION, MONOALLELIC EXPRESSION, UNIPARENTAL DISOMY, ALLELIC EXPRESSION, RNA, RESOLUTION, DISEASE

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MLA
Dini, Pouya, et al. “Parental Bias in Expression and Interaction of Genes in the Equine Placenta.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 118, no. 16, 2021, doi:10.1073/pnas.2006474118.
APA
Dini, P., Kalbfleisch, T., Uribe-Salazar, J. M., Carossino, M., Ali, H. E.-S., Loux, S. C., … Ball, B. A. (2021). Parental bias in expression and interaction of genes in the equine placenta. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 118(16). https://doi.org/10.1073/pnas.2006474118
Chicago author-date
Dini, Pouya, Theodore Kalbfleisch, José M. Uribe-Salazar, Mariano Carossino, Hossam El-Sheikh Ali, Shavahn C. Loux, Alejandro Esteller-Vico, et al. 2021. “Parental Bias in Expression and Interaction of Genes in the Equine Placenta.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 118 (16). https://doi.org/10.1073/pnas.2006474118.
Chicago author-date (all authors)
Dini, Pouya, Theodore Kalbfleisch, José M. Uribe-Salazar, Mariano Carossino, Hossam El-Sheikh Ali, Shavahn C. Loux, Alejandro Esteller-Vico, Jamie K. Norris, Lakshay Anand, Kirsten E. Scoggin, Carlos M. Rodriguez Lopez, James Breen, Ernest Bailey, Peter Daels, and Barry A. Ball. 2021. “Parental Bias in Expression and Interaction of Genes in the Equine Placenta.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 118 (16). doi:10.1073/pnas.2006474118.
Vancouver
1.
Dini P, Kalbfleisch T, Uribe-Salazar JM, Carossino M, Ali HE-S, Loux SC, et al. Parental bias in expression and interaction of genes in the equine placenta. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2021;118(16).
IEEE
[1]
P. Dini et al., “Parental bias in expression and interaction of genes in the equine placenta,” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 118, no. 16, 2021.
@article{8740485,
  abstract     = {{Most autosomal genes in the placenta show a biallelic expression pattern. However, some genes exhibit allele-specific transcription depending on the parental origin of the chromosomes on which the copy of the gene resides. Parentally expressed genes are involved in the reciprocal interaction between maternal and paternal genes, coordinating the allocation of resources between fetus and mother. One of the main challenges of studying parental-specific allelic expression (allele-specific expression [ASE]) in the placenta is the maternal cellular remnant at the fetomaternal interface. Horses (Equus caballus) have an epitheliochorial placenta in which both the endometrial epithelium and the epithelium of the chorionic villi are juxtaposed with minimal extension into the uterine mucosa, yet there is no information available on the allelic gene expression of equine chorioallantois (CA). In the current study, we present a dataset of 1,336 genes showing ASE in the equine CA (https://pouya-dini.github.io/equine-gene-db/) along with a work-flow for analyzing ASE genes. We further identified 254 potentially imprinted genes among the parentally expressed genes in the equine CA and evaluated the expression pattern of these genes throughout gestation. Our gene ontology analysis implies that maternally expressed genes tend to decrease the length of gestation, while paternally expressed genes extend the length of gestation. This study provides fundamental information regarding parental gene expression during equine pregnancy, a species with a negligible amount of maternal cellular remnant in its placenta. This information will provide the basis for a better understanding of the role of parental gene expression in the placenta during gestation.}},
  articleno    = {{e2006474118}},
  author       = {{Dini, Pouya and Kalbfleisch, Theodore and Uribe-Salazar, José M. and Carossino, Mariano and Ali, Hossam El-Sheikh and Loux, Shavahn C. and Esteller-Vico, Alejandro and Norris, Jamie K. and Anand, Lakshay and Scoggin, Kirsten E. and Rodriguez Lopez, Carlos M. and Breen, James and Bailey, Ernest and Daels, Peter and Ball, Barry A.}},
  issn         = {{0027-8424}},
  journal      = {{PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}},
  keywords     = {{allele-specific expression,parental gene expression,monoallelic gene expression,placenta,equine,GENOME-WIDE ANALYSIS,DNA METHYLATION,IMPRINTED GENE,ANTISENSE TRANSCRIPTION,MONOALLELIC EXPRESSION,UNIPARENTAL DISOMY,ALLELIC EXPRESSION,RNA,RESOLUTION,DISEASE}},
  language     = {{eng}},
  number       = {{16}},
  pages        = {{12}},
  title        = {{Parental bias in expression and interaction of genes in the equine placenta}},
  url          = {{http://doi.org/10.1073/pnas.2006474118}},
  volume       = {{118}},
  year         = {{2021}},
}
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