Analysis of Nr1h2 and H3K27ac genomic binding targets in ESC and EPSC under Nr1h2 activation
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ABSTRACT:
PROVIDER: PRJNA900609 | ENA |
REPOSITORIES: ENA
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Project description:ChIP-seq for Nr1h2 in NrESC, ESC. H3K27ac ChIP-seq in NrESC, ESC, EPSC, EPSCT09 Embryonic stem cells upon extrinsic induction could self-assemble into blastocyst-like structures. However, the intrinsic regulation of such blastoid forming potential remain to be addressed. We discover that the activity of nuclear receptor subfamily 1, group H, member 2 (Nr1h2) in expanded potential stem cell (EPSC) positively correlates with blastoid efficiency and quality. In addition, Nr1h2 agonist, T0901317, improves natural blastocyst development. Surprisingly, Nr1h2-activated ESC (NrESC) is rewired towards a distinct pluripotency state that is capable of self-organizing into blastoids and contribute to embryonic and extraembryonic lineage. We hypothesize that Nr1h2 activation broadly affects the transcriptome landscape by regulating chromatin accessibility and epigenome to rewire ESC state. Indeed, from Nr1h2 and H3K27Ac ChIP-seq, we observe that annotated genes with upregulated Nr1h2 binding as well as H3K27Ac marks in NrESC or EPSC treated with T09 are enriched in processes such as lipid metabolism, pluripotency maintenance and trophectoderm maturation, which are known to be essential to blastocyst development. In summary, our study demonstrates a novel Nr1h2-centric regulation of expanded pluripotency.
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Project description:ATAC-seq in NrESC_1, NrESC_16, ESC, EPSC Embryonic stem cells upon extrinsic induction could self-assemble into blastocyst-like structures. However, the intrinsic regulation of such blastoid forming potential remain to be addressed. We discover that the activity of nuclear receptor subfamily 1, group H, member 2 (Nr1h2) in expanded potential stem cell (EPSC) positively correlates with blastoid efficiency and quality. In addition, Nr1h2 agonist, T0901317, improves natural blastocyst development. Surprisingly, Nr1h2-activated ESC (NrESC) is rewired towards a distinct pluripotency state that is capable of self-organizing into blastoids and contribute to embryonic and extraembryonic lineage. We hypothesize that Nr1h2 activation broadly affects the transcriptome landscape by regulating chromatin accessibility and epigenome to rewire ESC state. Indeed, from ATAC-seq analysis, we observe some genomic regions progressively gained accessibility in NrESC over passages, which lead to a unique chromatin accessibility profile in NrESC compared to conventional ESC and EPSC. Binding motifs of Pou5f1, Sox2 and Tead4, which are known master regulator of blastocyst lineage specification, showed gained accessibility in NrESC. In summary, our study demonstrates a novel Nr1h2-centric regulation of expanded pluripotency in terms of chromatin reorganization.
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Project description:Translation and mRNA degradation are intimately connected, yet the mechanisms that regulate them are not fully understood. Here we examine the regulation of translation and mRNA stability in mouse embryonic stem cells (ESCs) and during differentiation. In contrast to previous reports, we found that transcriptional changes account for most of the molecular changes during ESC differentiation. Within ESCs translation level and mRNA stability are positively correlated. The RNA-binding protein DDX6 has been implicated in processes involving both translational repression and mRNA destabilization; in yeast DDX6 connects codon optimality and mRNA stability and in mammals DDX6 is involved in microRNA-mediated repression. We generated DDX6 KO ESCs and found that while there was minimal connection between codon usage and stability changes, the loss of DDX6 leads to the translational depression of microRNA targets. Surprisingly, the translational derepression of microRNA targets occurs without affecting mRNA stability. Furthermore, DDX6 KO ESCs share overlapping phenotypes and global molecular changes with ESCs that completely lack all microRNAs. Together our results demonstrate that the loss of DDX6 decouples the two forms of microRNA induced repression and emphasize that translational repression by microRNAs is underappreciated.
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