Super Enhancer Profiles Identify Key Cell Identity Genes During Differentiation From Embryonic Stem Cells to Trophoblast Stem Cells Super Enhencers in Trophoblast Differentiation.

Rongpu Jia,Song Guo,Yu Gao,Yijuan Huang,Chenyu Gou,Si Li,Meiqiong Fan,Liangji Zhou,Yuanqiu Chen

doi:10.3389/fgene.2021.762529

Abstract

Trophoblast stem cells (TSCs) are derived from blastocysts and the extra-embryonic ectoderm (ExE) of post-implantation embryos and play a significant role in fetal development, but the roles that TSCs play in the earlier status of fetal diseases need further exploration. Super enhancers (SEs) are dense clusters of stitched enhancers that control cell identity determination and disease development and may participate in TSC differentiation. We identified key cell identity genes regulated by TSC-SEs via integrated analysis of H3K27ac and H3K4me1 chromatin immunoprecipitation sequencing (ChIP-seq), RNA-sequencing (RNA-seq) and ATAC-sequencing (ATAC-seq) data. The identified key TSC identity genes regulated by SEs, such as epidermal growth factor receptor (EGFR), integrin β5 (ITGB5) and Paxillin (Pxn), were significantly upregulated during TSC differentiation, and the transcription network mediated by TSC-SEs enriched in terms like focal adhesion and actin cytoskeleton regulation related to differentiation of TSCs. Additionally, the increased chromatin accessibility of the key cell identity genes verified by ATAC-seq further demonstrated the regulatory effect of TSC-SEs on TSC lineage commitment. Our results illustrated the significant roles of the TSC-SE-regulated network in TSC differentiation, and identified key TSC identity genes EGFR, ITGB5 and Pxn, providing novel insight into TSC differentiation and lays the foundation for future studies on embryo implantation and related diseases.

Highlights

Trophoblasts play a significant role in embryonic development, and many studies have demonstrated that developmental disorders of trophoblasts are closely related to fetal diseases (Knöfler et al, 2019)
To understand the roles of Super enhancers (SEs) in the differentiated Trophoblast stem cells (TSCs), a chromatin immunoprecipitation sequencing (ChIPseq) analysis of H3K27ac and H3K4me1 was performed to investigate whether SEs regulate the enhanced differentiation of TSCs
SEs were identified by analyzing H3K27ac and H3K4me1 ChIPseq data, and crucial TSC identity genes were discovered through an integrated analysis with RNA-seq data

Summary

Introduction

Trophoblasts play a significant role in embryonic development, and many studies have demonstrated that developmental disorders of trophoblasts are closely related to fetal diseases (Knöfler et al, 2019). Understanding the key regulatory network involved in the processes of trophoblast stem cell (TSC) differentiation and gene expression is important for the further study of TSC differentiation, embryo implantation and embryonic development. The ICM has the potential to form an embryo, and the trophectoderm will develop into extraembryonic structures such as trophoblast stem cell and placenta (Pijnenborg et al, 1981; Gamage et al, 2016; Turco et al, 2018). The isolation of the trophectoderm and ICM is crucial for embryonic development and plays an important role in embryo implantation. Embryonic stem cells (ESCs) are derived from the ICM, possess multipotential differentiation potency, and can be acquired through separation and cultivation in vitro (Thomson et al, 1998); which make them an excellent model for research on TSC differentiation in vitro

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