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Transcriptional profiles of bovine in vivo pre-implantation development

ABSTRACT: During 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. Here we report the first transcriptome dynamics of single matured bovine oocytes and all stages of pre-implantation embryos developed in vivo. Surprisingly, nearly half of the bovine genome, 11,488 to 12,729 genes 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 activation occurs at this transition. Additionally, 774 genes were identified as only expressed/highly enriched in particular stages of development. 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 embryogenesis; yet, the majority of the hub genes are relatively unknown/under-studied in embryos. We also conducted the first embryonic expression profile comparison 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. This study provides the first comprehensive examination for gene activities in bovine embryos and identified little-known potential master regulators of pre-implantation development.

ORGANISM(S): Bos taurus

PROVIDER: GSE59186 | GEO | 2014/09/10

SECONDARY ACCESSION(S): PRJNA254699

REPOSITORIES: GEO

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Project description:During 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. Here we report the first transcriptome dynamics of single matured bovine oocytes and all stages of pre-implantation embryos developed in vivo. Surprisingly, nearly half of the bovine genome, 11,488 to 12,729 genes 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 activation occurs at this transition. Additionally, 774 genes were identified as only expressed/highly enriched in particular stages of development. 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 embryogenesis; yet, the majority of the hub genes are relatively unknown/under-studied in embryos. We also conducted the first embryonic expression profile comparison 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. This study provides the first comprehensive examination for gene activities in bovine embryos and identified little-known potential master regulators of pre-implantation development. RNA-Seq profiles from single in vivo matured oocytes and in vivo developed embryos from the 2-cell to the blastocyst stages generated using Solid RNA-seq platform.

Project description:Background:Maternal mRNAs that accumulate in the oocyte during oogenesis play important roles during initial stages of embryonic development, before activation of the embryonic genome. Parthenogenesis of mammalian is a critical research modle for the function analysis of maternal genomics. Results:Here we report comprehensive maternal transcriptome dynamics of single matured oocytes and pre-implantation embryos of buffalo parthenogenesis.Notably, more than half of the estimated 28659 bovine genes,15331 involved in more than 280 pathways, is expressed in oocytes and early embryos of parthenogenesis .The total numbers of genes expressed across stages are from 908 genes (morula/16cells)to 2603 genes(blastocyst/morula), and the nature of the expressed genes is also greatly different. A total of 3567 unique genes were identified to be differentially expressed between all consecutive stages of development(FPKM>0),of which the biggest expressed change was detected between the 8-and 16-cell stages, which demonstrated that parthenogenetic activation of embryonic development exist an embryonic genome activation process which is the same as the normal fertilization of embryos,also occurs between 8cells-16cells, consistent with the time of the development of the normal fertilized embryonic development,which suggesting that parthenogenetic embryonic development and normal fertilization embryo development may have a similar genome activation transcription regulation process.Besides,2726 genes were identified as only expressed/highly enriched in particular stages of development, suggesting their stage-specific roles in maternal genome during embryogenesis.Using weighted gene co-expression network analysis, we found 11 stage-specific modules of co-expressed genes that can be used to represent the corresponding stage of development. Furthermore, we identified 1530 hub genes of the maternally expressed gene networks. Methods:Maternal mRNA profiles of pre-implantation development in buffalo parthenogenesis,using single-cell RNA sequencing in IlluminaHiSeq platform. Sequencing adapters were trimmed using Cutadapt (https://code.google.com/p/cutadapt/) and the filtered reads were mapped to the reference genome sequence (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/471/725/GCA_000471725.1_UMD_CASPUR_WB_2.0/)assembly using Tophat2 followed by Cufflinks.qRT–PCR validation was performed using SYBR Green assays. Conclusions:This study provides a comprehensive examination of maternally expressed gene activities in buffalo oocytes and pre-implantation embryos of parthenogenesis for the first time,and find the special “EGA”between 8cells-16cells for parthenogenetic embry,and the study screen a number of specific stages hub gene with potentially important function.

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Transcriptional profiles of bovine in vivo pre-implantation development

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