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

Abstract

The objective of this study was to investigate the mechanism that regulates pre-implantation development of the yak (Bos grunniens). We determined the transcriptomes of in vitro-produced yak embryos at two-cell, four-cell, eight-cell stages, and morula and blastocyst using the Illumina RNA-seq for the first time. We obtained 47.36-50.86 million clean reads for each stage, of which, 85.65%-90.02% reads were covered in the reference genome. A total of 17,368 genes were expressed during the two-cell stage to blastocyst of the yak, of which 7,236 genes were co-expressed at all stages, whereas 10,132 genes were stage-specific expression. Transcripts from 9,827 to 14,893 different genes were detected in various developmental stages. When |log ratio| ≥ 1 and q-value <0.05 were set as thresholds for identifying differentially expressed genes (DEGs), we detected a total of 6,922-10,555 DEGs between any two consecutive stages. The GO distributions of these DEGs were classified into three categories: biological processes (23 terms), cellular components (22 terms) and molecular functions (22 terms). Pathway analysis revealed 310 pathways of the DEGs that were operative in early pre-implantation yak development, of which 32 were the significantly enriched pathways. In conclusion, this is the first report to investigate the mechanism that regulates yak embryonic development using high-throughput sequencing, which provides a comprehensive framework of transcriptome landscapes of yak pre-implantation embryos.

Transcriptional profiles of crossbred embryos derived from yak oocytes in vitro fertilized with cattle sperm

“…Our previous study 10 and qRT-PCR analyses of the amplified RNA in the present study (Fig. 5 ) verified that the Smart-seq2 accurately reflect the relative abundance of selected amplified transcripts ( SKP1 , CD63 , ZAR1 and H3 ) in the samples.…”

“…We identified ubiquitin-mediated proteolysis as enriched from the 2- to 4-cell and from the 8-cell to morula stages, and the most common pathway was RNA transport throughout the pre-implantation development of crossbred embryos of yak and cattle. In general, the pathways enriched by DEGs were not completely the same as those found in the bovine 8 , 16 , 49 , yak 10 , pig 6 , mouse and human 11 , 37 , 42 . Embryonic expression profiles across these mammalian species are different.…”

“…It occurs at the 2-cell stage in mice 26 , between the 4- and 8-cell stages in humans 27 and pigs 6 , 26 , and between the 8- and 16-cell stages in bovines 23 , 26 . Previous reports have alluded to minor bovine EGA between the zygote and 4-cell stage 10 , 16 , 28 – 31 . However, our previous report in the yak 10 and this data show that a high number of genes were significantly up-regulated between 2-cell and 4-cell stage, indicating that EGA occurs before the 8-cell stage in the yak and its crossbred embryos.…”

“…Previous reports have alluded to minor bovine EGA between the zygote and 4-cell stage 10 , 16 , 28 – 31 . However, our previous report in the yak 10 and this data show that a high number of genes were significantly up-regulated between 2-cell and 4-cell stage, indicating that EGA occurs before the 8-cell stage in the yak and its crossbred embryos. BMP15 , ZP3 , 4 , PPARG , SLBP , FRZB and KIT are oocyte markers 27 , 32 – 37 , and they were down-regulated with the development of the embryos (Fig.…”

“…The development of RNA sequencing technologies permits the study of gene regulation at an unprecedented level. Such studies have been successfully conducted in mouse 5 , pig 6 , cattle 7 , 8 , human 9 and yak 10 . However, these data have limited utility in crossbred embryogenesis of the yak due to the large differences in gene expression and genome sequences between different species 11 – 13 .…”