RNA-Seq Transcriptome Profiling of Equine Inner Cell Mass and Trophectoderm1

Abstract

Formation of the inner cell mass (ICM) and trophectoderm (TE) marks the first differentiation event in mammalian development. These two cell types have completely divergent fates for the remainder of the developmental process. The molecular mechanisms that regulate ICM and TE formation are poorly characterized in horses. The objective of this study was to establish the transcriptome profiles of ICM and TE cells from horse blastocysts using RNA sequencing (RNA-seq). A total of 12 270 genes were found to be expressed in either lineage. Global analysis of the transcriptome profiles by unsupervised clustering indicated that ICM and TE samples presented different gene expression patterns. Statistical analysis indicated that 1662 genes were differentially expressed (adjusted P < 0.05 and fold change > 2) between ICM and TE. Genes known to be specific to the ICM and TE were expressed primarily in their respective tissue. Transcript abundance for genes related to biological processes important for horse blastocyst formation and function is presented and discussed. Collectively, our data and analysis serve as a valuable resource for gene discovery and unraveling the fundamental mechanisms of early horse development.

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

“…The newly reported transcripts were connected to overall biological processes like transcription. 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).…”

“…The obtained results have shown higher expression of genes coding blastocyst mucin (MUC1, MUC20), key enzymes catalyzing sialic acid biosynthesis (NAGK, NANS, CMAS, GNE), enzymes responsible for GalNAc metabolism (B3GNT2, B3GALNT1, ST3GAL4, GLT8D1), UDP-galactose transporters (SLC35A2, SLC35A3, SLC35A4), and genes involved in the synthesis of proteoglycan (GLANT gene family). The higher transcript abundance was also observed for genes coding enzymes involved in the biosynthesis of sulfated sugars genes, such as carbohydrate sulfotransferases (CHST), heparan sulfotransferases (HS2ST1), and transglutaminases (TGM3) (Iqbal et al 2014). The identification of gene expression patterns involved in blastocyst formation will broaden the existing knowledge and provide a foundation for further studies of mammalian embryology.…”

“…The comprehensive analysis of gene expression has been performed on inner cell mass (ICM, embryoblast) and trophectoderm from horse blastocysts (Iqbal et al 2014). ICM differentiates into ectoderm, mesoderm, and endoderm, while trophectoderm contributes to the development of placenta tissues.…”

DPPA3 prevents cytosine hydroxymethylation of the maternal pronucleus and is required for normal development in bovine embryos

“…30,31 Briefly, 3-4 groups of 10 in vitro matured oocytes and in vitro produced embryos were used per stage of development. In a group of embryos, α-amanitin was added at the zygote stage at 50 μg/ ml and 8-cell embryos collected 56 h post fertilization.…”

Genetic Susceptibility to Rhodococcus equi

“…A subsequent study focused on characterizing gene expression by RNA‐Seq in immunologically active tissues 95. Investigators have used RNA‐Seq to characterize the expression profile of genes critical to the differentiation and regulation of cells during embryogenesis,90 and to characterize the expression and inferred function of RNAs in the equine sperm transcriptome 89. Several studies also have used RNA‐Seq in horses to identify differentially expressed genes when comparing blood, muscle (obtained by biopsy), or both before and after exercise or racing 86, 87, 92.…”