Super-enhancer-guided decoding of gene regulatory networks in trophoblast stem cells

Cells belonging to trophoblast lineage are required for proper implantation and placentation, as well as the vascular, hematopoietic, and immunological properties of the placenta, a crucial organ mediating dynamic interactions between maternal and fetal tissues. Defects in trophoblast lineage development can cause early pregnancy failure or other pregnancy-related disorders. Despite its pivotal roles, the placenta remains as one of the least studied organs. Until now, only a handful of trophoblast-specific transcription factors (TFs) have been characterized, and underlying regulatory mechanisms modulating trophoblast lineage development remain poorly understood. Here we explore trophoblast stem cell (TSC)-specific super-enhancers (SEs) and subsequently identify SE-associated factors enriched with previously known and many unknown TFs modulating trophoblast lineage development. By mapping direct targets of 28 TSC-specific TFs in TSCs, we construct highly intertwined transcriptional regulatory networks where TFs are co-regulated and linked with signaling pathways, and which function as cellular modules dedicated to trophoblast lineage development. Additionally, we reveal that TSC-specific TFs alter their target sites corresponding to the reshaped enhancers during TSC differentiation. These findings advance our understanding on placenta biology. Overall design: ChIP sequenicngs were performed for p300, Med12, various trophoblast-specific transcription factors, and diverse histone marks using native antibodies in self-renewing and differentiated trophoblast stem cells (TSCs). Mock ChIP was also performed for a control. ATAC-seq was performed for both self-renewing embryonic stem cells(ESCs) and TSCs. RNA-seq was performed with samples from knockdown of either Meis1, Hopx, Maff, Mafk, Pou3f1, and a control in both TSC and differentiated TSCs (dTSCs) for 3 days.