Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Characterization of gene expression involved in pig reproduction

ABSTRACT: Purpose: Recent development in high-throughput sequencing techniques (RNA-seq) has enabled large scale analysis of genetic variations and gene expression in different tissues and species, but gene expression patterns and genetic variations in livestock have not yet been well characterized. In this study we have used high-throughput transcriptomic sequencing of the Finnish Yorkshire to identify gene expression patterns within the breed in the testis and oviduct. Methods: The Solid 4 reads were mapped against the pig genome build 10.2 using the colorspace alignment tool provided by Applied Biosystems and distributed with the instrument (LifeScope v2.1). Reads associated with ribosomal RNA, transfer RNA, repeats and other uninformative reads were filtered out during the process as well as reads with more than 10 potential alignments. After alignment to the reference genome, low mapping quality reads were discarded (mapQV(<10)) and unique reads were associated with known genes based on UCSC annotations, and the number of reads aligned within each gene was counted. FPKM values were calculated for normalization of the data to remove variation between samples caused by non-biological reasons using the Cufflinks software v2.0.2. Results: The analysis of gene expression differences between the testis and oviduct highlighted 1,234 genes up-regulated in the testis and 1,501 in the oviduct. Conclusions: The RNA-seq technology used in this study provides novel information about transcript expression and differential gene expression in the testis and oviduct. The produced data will assist in the identification of candidate genes based on association mapping results within the pig population and provides insights into the expression of genes in the two reproductive organs studied. Testis and oviduct mRNA profiles of adult WT and immotile short tail sperm (ISTS) affected Finnish Large White pigs were generated by deep sequencing using Solid 4 platform.

ORGANISM(S): Sus scrofa

SUBMITTER: Anu Sironen

PROVIDER: E-GEOD-59149 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of Reproduction-Related Gene Polymorphisms Using Whole Transcriptome Sequencing in the Large White Pig Population.

Fischer Daniel D Fischer Daniel D Laiho Asta A Gyenesei Attila A Sironen Anu A

G3 (Bethesda, Md.) 20150427 7

Recent developments in high-throughput sequencing techniques have enabled large-scale analysis of genetic variations and gene expression in different tissues and species, but gene expression patterns and genetic variations in livestock are not well-characterized. In this study, we have used high-throughput transcriptomic sequencing of the Finnish Large White to identify gene expression patterns and coding polymorphisms within the breed in the testis and oviduct. The main objective of this study ...[more]

PMID: 25917919

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Project description:Ciliary action performs a critical role in the oviduct (Fallopian tube), during pregnancy establishment through sperm and egg transport. The disruption of normal ciliary function in the oviduct affects oocyte pick-up and is a contributing factor to female infertility. Estrogen is an important regulator of ciliary action in the oviduct and promotes ciliogenesis in several species. Global loss of estrogen receptor 1 alpha (encoded by Esr1 gene) leads to infertility. Our laboratory has previously shown that ESR1 in the oviductal epithelial cell layer is required for female fertility. Here, we assessed the role of estrogen on transcriptional regulation of ciliated epithelial cells of the oviduct using single-cell RNA-sequencing analysis. We observed minor variations in ciliated cell genes in the proximal region (isthmus and uterotubal junction) of the oviduct. However, E2 treatment had little impact on the gene expression profile of ciliated epithelial cells. To assess the requirement of ESR1 specifically in ciliated cells for female fertility, we conditionally ablated Esr1 from ciliated epithelial cells of the oviduct (called ciliated Esr1d/d mice). Our studies showed that ciliated Esr1d/d females had fertility rates comparable to control females, did not display any disruptions in preimplantation embryo development or embryo transport to the uterus, and had comparable cilia formation to control females. However, we observed some incomplete deletion of Esr1 in the ciliated epithelial cells, especially in the ampulla region. Therefore, more studies are required to definitively determine ESR1 function in ciliated cells of the oviduct. Nevertheless, our data suggest that ESR1 expression in ciliated cells of the oviduct is dispensable for ciliogenesis, but nonessential for female fertility in mice. All genes expressed in scRNA-seq datasets are available for scientific community and separable at https://www.winuthayanon.com/genes/ve2h_cilia/ and https://www.winuthayanon.com/genes/ve2h_allclusters/

Dataset Information

Characterization of gene expression involved in pig reproduction

Publications

Identification of Reproduction-Related Gene Polymorphisms Using Whole Transcriptome Sequencing in the Large White Pig Population.

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