Transcriptomic analysis reveals differential gene expression, alternative splicing, and novel exons during mouse trophoblast stem cell differentiation

Rahim Ullah,Amir Faisal,Zakir Ullah,Hafiza Sara Akram,Aziz Mithani,Muhammad Tariq,Ambreen Naz

doi:10.1186/s13287-020-01848-8

Abstract

BackgroundDifferentiation of mouse trophoblast stem cells (TSCs) to trophoblast giant cells (TGCs) has been widely used as a model system to study placental development and function. While several differentially expressed genes, including regulators of TSC differentiation, have been identified, a comprehensive analysis of the global expression of genes and splice variants in the two cell types has not been reported.ResultsHere, we report ~ 7800 differentially expressed genes in TGCs compared to TSCs which include regulators of the cell cycle, apoptosis, cytoskeleton, cell mobility, embryo implantation, metabolism, and various signaling pathways. We show that several mitotic proteins, including Aurora A kinase, were downregulated in TGCs and that the activity of Aurora A kinase is required for the maintenance of TSCs. We also identify hitherto undiscovered, cell-type specific alternative splicing events in 31 genes in the two cell types. Finally, we also report 19 novel exons in 12 genes which are expressed in both TSCs and TGCs.ConclusionsOverall, our results uncover several potential regulators of TSC differentiation and TGC function, thereby providing a valuable resource for developmental and molecular biologists interested in the study of stem cell differentiation and embryonic development.

Highlights

Differentiation of mouse trophoblast stem cells (TSCs) to trophoblast giant cells (TGCs) has been widely used as a model system to study placental development and function
Differentiation of trophoblast stem cells into trophoblast giant cells Trophoblast stem cells with diploid genomes are smaller in size and form compact colonies
Once the differentiation of TSCs was induced by removing fibroblast growth factor 4 (FGF4) from the medium, the cells became progressively larger with very heterogeneous shape, size, and ploidy level (Fig. 1), as described previously [15]

Summary

Introduction

Differentiation of mouse trophoblast stem cells (TSCs) to trophoblast giant cells (TGCs) has been widely used as a model system to study placental development and function. Trophectoderm exclusively gives rise to the placenta, Mouse trophoblast stem cells (TSCs) are derived from the polar trophectoderm of the blastocyst [1] and have been widely used to study placental development [4,5,6]. The differentiation of TSCs into TGCs is regulated by a number of factors including cytokines, hormones, protein kinases, transcription factors, proteases, and membrane proteins [9,10,11,12,13,14,15,16]. Removal of fibroblast growth factor 4 (FGF4) from TSC culture

Methods

Results

Conclusion