Mapping Potency States of Stem Cells
Embryonic stem cells (ESCs) effectively repress the expression of exogenous proviruses and endogenous retroviruses (ERVs). In our earlier work, we systematically dissected the cellular factors involved in provirus repression in ESCs through a genome-wide siRNA screen (Yang et al, Cell 2015). This investigation revealed that histone chaperones (Chaf1a/b), sumoylation factors (Sumo2/Ube2i), and chromatin modifiers (Trim28/Eset/Atf7ip) are crucial determinants in establishing provirus and ERV silencing. Further analysis determined that Chaf1a enhances transcriptional repression through its interactions with members of the NuRD complex (Kdm1a, Hdac1/2) and Eset, while Sumo2 facilitates the proviral repressive function of the canonical Zfp809/Trim28/Eset machinery by sumoylating Trim28. This study is significant because MERVL, a class 2 ERV, is known to be repressed in the pluripotent ESC state but activated during the totipotent-like states of the 2-cell stage. Hence, the factors we identified, Chaf1a/b, Sumo, Trim28, Eset and Zmym2, act as guardians that prevent the spontaneous “reversion” of ESCs to an earlier totipotent state.
Indeed, the co-evolution of repeat elements, including Transposable elements (TE) and ERVs, and their regulators such as KRAB-ZFPs, has influenced genome formation throughout evolution. However, the functions and roles of these repeat elements in normal cellular processes remain largely enigmatic (Gautam et al. Curr Opin Genet Dev. 2017). In a collaborative study with Andrew Hutchins’s lab, the team identified 29 epigenetic modifiers that significantly influence TE regulation; the loss of specific modifiers, such as Eset, Ncor2, and Rnf2, resulted in variable changes in TE expression. These context-specific effects suggest that different chromatin modifiers regulate distinct subsets of TEs, highlighting the complexity of their epigenetic regulation (He et al Nat Commun. 2019).
Many transposable elements (TEs) are integrated into the genome and function as TE-derived enhancers. In our recent study (Cipta et al., Genome Biology 2025), we investigated whether TE-enhancer could regulate cell state-specific gene expression in naïve and expanded pluripotent embryonic stem (ES) cell states. We found that the mammalian-wide interspersed repeat (MIR), a SINE family member, is significantly associated with naïve state-specific genomic interactions. In the naïve pluripotent state, the MIR enhancer interacts with Esrrb to drive a naïve-specific gene expression program, forming loops that link enhancers and super-enhancers that regulate pluripotency genes. The loss of the Esrrb-bound MIR enhancer impairs self-renewal. Given that MIR is a TE shared among all mammalian species, investigating its co-option by Esrrb may provide insights into the evolution of placental mammals (Cipta et al., Genome Biology 2025).
Recent advancements in the stem cell field have been propelled by the ability to create early embryonic organoid models, which provide invaluable platforms for studying embryogenesis and progenitor cell fate development. The capacity to generate early embryos and chimeric embryos from different species underscores the importance of approaching this area with caution due to ethical concerns and its significant potential, a topic we explored in detail with our international stem cell colleagues (Los Angeles et al., Nat Methods 2022). The specific intrinsic regulators driving the formation of embryo-like structures, known as blastoids, from ESCs remain largely unknown. Our research demonstrates a crucial intrinsic program that influences both blastoids and blastocysts across multiple species (Wong et al., Nat Commun. 2024). We found that the disruption of nuclear receptor subfamily 1, group H, member 2 (Nr1h2) significantly hampers blastoid formation. Activation of Nr1h2 by its agonist drug on the other hand, can reprogram conventional ESCs into a distinct expanded pluripotent state, allowing for the formation of blastoids with improved implantation capacity in the uterus and the ability to contribute to both embryonic and extraembryonic lineages in vivo. Through integrative multi-omics analyses, we revealed the extensive regulatory role of Nr1h2 in shaping the transcriptome, chromatin accessibility, and epigenome, specifically targeting genes associated with embryonic lineage and the transposable element SINE-B1. This Nr1h2-centered intrinsic program is fundamental in driving the development of both blastoids and early embryos (Fig 2) (Wong et al., Nat Commun. 2024). Our findings hold significant implications for improving embryo models and suggest the potential of Nr1h2 agonists as therapeutic candidates for improving IVF, which are planning to move into in the next phase of the project (IP: Novel Method to Enhance Synthetic Embryo Formation and Multi-Species Embryos Development Using Nr1h2 Drug). Collectively, our investigations into the interactions between regulatory factors and transposable elements (TE) within the genome have elucidated the mechanisms that govern the distinct states of stem cell potency.
Other studies from our research in the field of stem cell potency have elucidated various important roles of ribosomal proteins in regulating the 2-cell stage transcriptome in ESCs (Yi et al., Stem Cell Reports, 2023). Additionally, we identified the non-canonical role of ESET, a key regulator of lineage-specific genes and endogenous retroviruses (ERVs), as a topological accessory to Cohesin, influencing the 3D structure of embryonic stem cells (Warrier et al., Nucleic Acids Res., 2022). Furthermore, essential enhancers for pluripotent stem cells have been defined using CRISPR-Cas screening (Wang et al., Cell Reports, 2020), role of PRDM15 in regulating naive pluripotency by modulating the WNT and MAPK-ERK signaling pathways is clarified (Mzoughi et al Nat Genet. 2017), and the regulation of stem cell metabolism and conversion to primed pluripotency by Lin28 has also been characterized (Zhang et al., Cell Stem Cell, 2016).