RNA-seq analysis of single bovine blastocysts

Abstract

BackgroundUse of RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to assay the developing embryo, but the paucity of biological material available from individual embryos has made this a challenging prospect.ResultsWe report here the first application of RNA-Seq for the analysis of individual blastocyst gene expression, SNP detection, and characterization of allele specific expression (ASE). RNA was extracted from single bovine blastocysts (n = 5), amplified, and analyzed using high-throughput sequencing. Approximately 38 million sequencing reads were generated per embryo and 9,489 known bovine genes were found to be expressed, with a high correlation of expression levels between samples (r > 0.97). Transcriptomic data was analyzed to identify SNP in expressed genes, and individual SNP were examined to characterize allele specific expression. Expressed biallelic SNP variants with allelic imbalances were observed in 473 SNP, where one allele represented between 65-95% of a variant’s transcripts.ConclusionsThis study represents the first application of RNA-seq technology in single bovine embryos allowing a representation of the embryonic transcriptome and the analysis of transcript sequence variation to describe specific allele expression.

RNA sequencing as a powerful tool in searching for genes influencing health and performance traits of horses

“…In general, the obtained results correspond to those commonly reported in other species (Iqbal et al 2014). However, it is noteworthy that the authors confirmed the possibility of identifying the sex of an embryo by comparing the levels of XIST (X inactive specific transcript, non-coding protein) previously reported in bovine embryos (Chitwood et al 2013). Furthermore, the transcriptome data have been analyzed according to pathways that may be involved in the creation of equine capsule.…”

RNA sequencing and transcriptome analysis of buffalo (Bubalus bubalis) blastocysts produced by somatic cell nuclear transfer and in vitro fertilization

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