Transcriptional profiles of bovine in vivo pre-implantation development

Abstract

BackgroundDuring mammalian pre-implantation embryonic development dramatic and orchestrated changes occur in gene transcription. The identification of the complete changes has not been possible until the development of the Next Generation Sequencing Technology.ResultsHere we report comprehensive transcriptome dynamics of single matured bovine oocytes and pre-implantation embryos developed in vivo. Surprisingly, more than half of the estimated 22,000 bovine genes, 11,488 to 12,729 involved in more than 100 pathways, is expressed in oocytes and early embryos. Despite the similarity in the total numbers of genes expressed across stages, the nature of the expressed genes is dramatically different. A total of 2,845 genes were differentially expressed among different stages, of which the largest change was observed between the 4- and 8-cell stages, demonstrating that the bovine embryonic genome is activated at this transition. Additionally, 774 genes were identified as only expressed/highly enriched in particular stages of development, suggesting their stage-specific roles in embryogenesis. Using weighted gene co-expression network analysis, we found 12 stage-specific modules of co-expressed genes that can be used to represent the corresponding stage of development. Furthermore, we identified conserved key members (or hub genes) of the bovine expressed gene networks. Their vast association with other embryonic genes suggests that they may have important regulatory roles in embryo development; yet, the majority of the hub genes are relatively unknown/under-studied in embryos. We also conducted the first comparison of embryonic expression profiles across three mammalian species, human, mouse and bovine, for which RNA-seq data are available. We found that the three species share more maternally deposited genes than embryonic genome activated genes. More importantly, there are more similarities in embryonic transcriptomes between bovine and humans than between humans and mice, demonstrating that bovine embryos are better models for human embryonic development.ConclusionsThis study provides a comprehensive examination of gene activities in bovine embryos and identified little-known potential master regulators of pre-implantation development.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-756) contains supplementary material, which is available to authorized users.

RNA‐Seq profiling of single bovine oocyte transcript abundance and its modulation by cytoplasmic polyadenylation

“…In agreement with a previous study (Jiang et al, ), we found that approximately half of all annotated protein‐coding genes are expressed in bovine oocytes. More of these genes were detected in GV‐ than in MII‐stage oocytes, with a large proportion of these genes decreasing in abundance compared to those that increased as maturation proceeded; similar trends were observed in other studies utilizing oocytes from bovine (Fair et al, ; Mamo et al, ), human (Assou et al, ), and Xenopus tropicalus (Graindorge et al, ).…”

Effect of vitrification on the mRNA transcriptome of bovine oocytes

“…The percentage of mapped reads ranged from 90.22% to 92.81%, and the rate of clean Q30 bases ranged from 94.70% to 95.94% (Table S1). The total numbers of detectable genes ranged from 11,772 to 12,655 in the control and vitrification groups (Table , Table S2), and were similar to those reported previously for bovine oocytes (Jiang et al., ).…”

Characterization of transcriptional complexity during pre‐implantation development of the yak (Bos grunniens) using RNA‐Seq

“…A total of 9,827–14,893 transcripts were detected in each in vitro stage (Table ). In general, this result was very similar to the findings in in vivo bovine embryos, but a much lower number of transcripts were detected at the blastocyst stage compared with the transcriptomes of bovine embryos (Graf et al., ; Jiang et al., ; Kues et al., ). This might reflect the suboptimal conditions of current IVC system for yak embryos.…”

“…The development of RNA sequencing technologies permits the study of gene regulation at an unprecedented level. Most studies have been conducted in the mouse, human and bovine (Cao et al., ; Graf et al., ; Jiang et al., ; Xie et al., ); however, regulation of yak embryonic gene expression still remains poorly understood. The application of RNA‐Seq in embryos is limited by the low RNA content of a single pre‐hatching bovine embryo (200–2,300 pg) depending on the stage of the development (Gilbert et al., ).…”