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Functional dissection of enhancers in 2-Cell embryo with an in vitro model [ChIP-seq]

ABSTRACT: Zygotic genome activation (ZGA) marks the initial transcription event in embryogenesis, yet the mechanisms cis-regulating gene activation remain unclear due to material constraints. Here, we functionally dissect the enhancers across the mouse genome in DUX-induced 2C-like cells. Integrated analysis with the epigenetic modifications and RNA transcriptiome in both 2C-like cells and 2C embryos, regions which show enhancer activities and their potential downstream target gens were depicted. Among them, a notable proportion of promoters exhibits enhancer activities in totipotent cells. Those promoter regions are characterized by elevated levels of open chromatin-associated epigenetic modifications, which correlate with enhanced gene expression during ZGA. Our data further reveal that class Ⅲ mouse endogenous retrovirus (MERV)-related enhancers are enriched in 2C-like cells and nearly half of MERVL-LTR (Mt2_mm) elements exhibit enhancer activities, which have been mapped and characterized within the genome. Intriguingly, enhancers identified in 2C-like cells augment the transcription in vivo when injected into the embryos. Furthermore, the deletion of enhancer regions in both 2C-like cells and embryos demonstrated their role in promoting the transcription of their adjacent downstream target genes, with one of the deletions impaired the early embryo development. This study enhances our understanding of the regulatory elements guiding ZGA.

ORGANISM(S): Mus musculus

PROVIDER: GSE283347 | GEO | 2026/07/27

REPOSITORIES: GEO

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Functional dissection of enhancers in 2-Cell embryo with an in vitro model [STARR-seq]

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Project description:Acquisition of new stem cell fates relies on the dissolution of the prior regulatory network sustaining the existing cell fates. Currently, extensive insights have been revealed for the totipotency regulatory network around the zygotic genome activation (ZGA) period. However, how the dissolution of the totipotency network is triggered to ensure the timely embryonic development following ZGA is largely unknown. In this study, we identified the unexpected role of a highly expressed 2C embryo specific transcription factor, ZFP352, in facilitating the dissolution of the totipotency network. We found that ZFP352 has bifurcated binding and regulation towards two different retrotransposon sub-families. ZFP352 coordinates with DUX to bind and regulate the 2C specific MT2_Mm sub-family. On the other hand, without DUX, ZFP352 switched affinity to bind extensively onto SINE_B1/Alu sub-family. This leads to the activation of later developmental programs like ubiquitination pathways, to facilitate the dissolution of the 2C state. Correspondingly, depleting ZFP352 in mouse embryos impaired the 2C to morula transition process. Thus, through differential regulation of MT2_Mm and SINE_B1/Alu, ZFP352 can trigger spontaneous dissolution of the totipotency network. Our study highlights the importance of different retrotransposons sub-families in facilitating the timely and programmed cell fates transition during early embryogenesis.

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USP17L promotes the 2-cell program through deubiquitination of H2AK119ub1 and ZSCAN4 [ChIP-Seq]

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