Super-enhancer-associated transcription factors collaboratively regulate trophoblast-active gene expression programs in human trophoblast stem cells

Abstract

The placenta is an essential organ that supports the growth and development of the fetus during pregnancy. However, cell type-specific enhancers and transcription factors (TFs), and the mechanisms underlying the maintenance and differentiation of trophoblast stem cell (TSC) populations in the human placenta remain elusive. Here, using human TSCs as a model system, we identify 31,362 enhancers that are enriched with the motifs of previously reported TSC-pivotal TFs, including TEAD4, GATA2/3 and TFAP2C. Subsequently, we identify 580 super-enhancers (SEs) and 549 SE-associated genes. These genes are robustly expressed in the human placenta and include numerous TFs, implying that SE-associated TFs (SE-TFs) may play crucial roles in placental development. Additionally, we identify the global binding sites of five TSC-pivotal SE-TFs (FOS, GATA2, MAFK, TEAD4 and TFAP2C), revealing that they preferentially co-occupy enhancers, regulate each other and form a trophoblast-active gene regulatory network. Loss-of-function studies unveil that the five TFs promote self-renewal of TSCs by activating proliferation-associated genes while repressing developmental genes. We further reveal that the five TFs exert conserved and unique functions on placental development between humans and mice. Our study provides important insights into the roles of human TSC-pivotal TFs in regulating placenta-specific gene expression programs.

Dynamic and distinct histone modifications facilitate human trophoblast lineage differentiation

“…Among the broad H3K4me3 domain-associated genes, we identified 139, 139, and 184 transcription factors (TFs) in TSCs, STs, and EVTs, respectively (Supplementary Table 3 ). These TFs included almost all of the previously reported human trophoblast regulators, including GATA2 33 , GATA3 34 , GCM1 35 , ASCL2 32 , MSX2 36 , TBX3 31 , EP300 37 , ELF3 38 , BHLHE40 39 , HIF1a 40 , TEAD4 30 , TWIST 41 as well as numerous uncharacterized TFs in human trophoblasts. These findings indicate that broad H3K4me3 can serve as a valuable tool for identifying novel trophoblast lineage-specific TFs.…”

Single-cell insights into development of the bovine placenta

“…Further, all transcription factors predicted to be involved in trophoblast fate in the mature bovine placenta were identified in the present study [35]. Eight transcription factors (JUN, YY1, BHLHE40, GATA2, GATA3, NR2F2, TFAP2A, TFAP2C) were predicted to be involved in UNC to BNC differentiation in the mature bovine placenta and are directly linked to trophoblast differentiation and function in other mammals [66–68]. The transcription factor with the greatest percent of total DEGs was CTCF, which regulates pregnancy-specific glycoprotein ( PSG1 , PSG2 , PSG4 , PSG5 , PSG6 , PSG8 , PSG9 , PSG11 ) expression in a human trophoblast cell line [69].…”

NOTCH3 signalling controls human trophoblast stem cell expansion and differentiation

“…For example, single cell analyses of primary tissues, TSCs and TB-ORGs gave novel insights into underlying mechanisms, the diversity of trophoblasts and their putative interactions with other placental and decidual cell types (Arutyunyan et al, 2023;Liu et al, 2018;Shannon et al, 2022;Vento-Tormo et al, 2018). Chromatin immunoprecipitation and sequencing has allowed to establishing a landscape of TSC enhancers that harbour binding sites for pivotal transcriptions factor of trophoblast development (Frost et al, 2023;Kim et al, 2023). Moreover, integrated bioinformatics of diverse data sets have suggested signalling molecules and networks that likely play major roles in trophoblast self-renewal (Chen et al, 2022;Cox and Naismith, 2022).…”

“…For instance, HIF, ASCL2, GCM1, and TCF4 have been identified as crucial regulators of EVT differentiation (Jeyarajah et al, 2022;Meinhardt et al, 2014;Varberg et al, 2021;Wakeland et al, 2017), whereas factors such as TEAD4, GATA2, MSX2 and TFAPC promote TSC selfrenewal (Chen et al, 2022;Hornbachner et al, 2021;Kim et al, 2023;Saha et al, 2020).…”

“…Transcriptional co-activators, i.e. enhancer-associated p300, and the HIPPO factors TAZ and YAP, are also critical for trophoblast stemness, the latter actively repressing genes associated with cell fusion (Kim et al, 2023;Meinhardt et al, 2020;Ray et al, 2022).…”