Endogenous retrovirus MER50-derived enhancers confer the transcriptional regulation of human trophoblast syncytialization [RNA-Seq]

Multinucleated syncytiotrophoblasts (STBs), which are in direct contact with maternal blood, constitute the maternal-fetal interface critical for nutrient allocation, hormone production and immunological modulation during pregnancy. However, the genetic and epigenetic regulatory mechanisms governing trophoblast syncytialization remain largely elusive. We delineate that endogenous retroviruses (ERVs), which have been exapted as regulatory sequences for specific functional adaptations in placenta, profoundly rewire transcriptional program of trophoblast syncytialization. Here, we first determined dynamic bivalent ERV-derived enhancers with dual occupancy of H3K9me3 and H3K27ac in human trophoblast stem cells (hTSCs), which emerge as cell specific regulators of gene expression with markedly resolved H3K9me3 during differentiation towards STBs. Of note, bivalent enhancers derived from the Simiiformes-specific MER50 transposons were linked to a cluster of STB-specific genes. Importantly, depletions of MER50 elements adjacent to several STB genes, including MFSD2A, TNFAIP2 and RAI14, significantly attenuated their expression concomitant to dysregulated syncytium formation. Together, we propose that ERV-derived enhancers, MER50 specifically, fine-tune the transcriptional program accounting for human trophoblast syncytialization, which sheds light on novel epigenetic regulatory mechanisms underlying placental development. We generated ChIP-Seq and RNA-Seq data in this study. ChIP-Seq data are for H3K27ac, H3K4me3 in hTSC (human trophoblast stem cell) and differentiated STB(syncytiotrophoblast) at 24h, 48h. RNA-Seq data are for hTSC and STB at four time points: 24h, 48h, 72h, 96h.

多核合体滋养层细胞（Multinucleated syncytiotrophoblasts，STBs）直接与母体血液接触，是构成妊娠期间关键母胎界面（maternal-fetal interface）的核心组分，该界面对于营养分配、激素产生与免疫调控至关重要。然而，调控滋养细胞合胞体化的遗传与表观遗传调控机制仍未得到充分阐明。我们的研究表明，内源性逆转录病毒（endogenous retroviruses，ERVs）——这类已被共招募为调控序列以实现胎盘特定功能适应的元件——可显著重编程滋养细胞合胞体化的转录程序。本研究首先在人类滋养层干细胞（human trophoblast stem cells，hTSCs）中鉴定出同时结合H3K9me3与H3K27ac的动态二价内源性逆转录病毒来源增强子；这类增强子在向多核合体滋养层细胞分化过程中，其H3K9me3修饰显著解除，成为细胞特异性基因表达调控因子。值得注意的是，源自类人猿亚目（Simiiformes）特异性MER50转座子的二价增强子，与一组多核合体滋养层细胞特异性基因密切关联。尤为关键的是，敲除多个多核合体滋养层细胞特异性基因（包括MFSD2A、TNFAIP2与RAI14）旁侧的MER50元件后，这些基因的表达显著下调，同时合胞体形成出现异常。综上，我们提出内源性逆转录病毒来源的增强子（尤以MER50为代表）可精细调控介导人类滋养细胞合胞体化的转录程序，这为阐明胎盘发育背后的新型表观遗传调控机制提供了全新视角。本研究生成了ChIP-Seq与RNA-Seq两类高通量测序数据：其中ChIP-Seq数据检测了人类滋养层干细胞（hTSC）以及分化24h、48h的多核合体滋养层细胞中的H3K27ac与H3K4me3修饰；RNA-Seq数据则涵盖人类滋养层干细胞以及分化24h、48h、72h、96h的多核合体滋养层细胞。