Self-organization of pluripotent stem cells into reproducible early embryonic developmental patterns through epigenome editing
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1078322 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28026257_1.fastq.gz | Fastqsanger.gz | |||
| SRR28026257_2.fastq.gz | Fastqsanger.gz | |||
| SRR28026258_1.fastq.gz | Fastqsanger.gz | |||
| SRR28026258_2.fastq.gz | Fastqsanger.gz | |||
| SRR28026259_1.fastq.gz | Fastqsanger.gz |
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Project description:During embryonic development, different embryonic cell types co-develop together where each cell type expresses specific fate-inducing transcription factors through activation of developmental non-coding regulatory elements and interactions with neighboring cells. Here, we hypothesized that cell-intrinsic activation of a minimum number of such endogenous regulatory elements is sufficient to self-organize PSCs into early embryonic models. Our results show that CRISPR activation of only two regulatory elements in the genome of pluripotent stem cells is sufficient to generate embryonic patterns that show spatial and molecular resemblance to that of pre-gastrulation mouse embryonic development. Quantitative single-cell live fluorescent imaging showed that emergence of the spatially-ordered embryonic pattern happens through intrinsic induction of cell fate that leads to an orchestrated collective cellular motion. Based on these results, we propose a straightforward approach to efficiently form 3D embryo models through intrinsic CRISPRa-based epigenome editing and independent of external signaling cues. CRISPRa-induced embryo models show highly consistent composition of major embryonic cell types that are spatially organized, with nearly 80% of the structures forming an embryonic cavity. Single cell transcriptomics confirmed the presence of main embryonic cell types in CRISRPa-induced embryo models with transcriptional similarity to pre-gastrulation mouse embryos and revealed novel signaling communication links between different embryonic cell types. Our findings demonstrate that self-organization of embryonic patterns through minimum intrinsic epigenome editing presents a promising approach for efficient production of stem cell-based embryo models with high consistency and will pave the way for future straightforward systematic CRISPR-based screening of embryo models
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Project description:Embryonic stem cells (ESCs) can self-organize in vitro into developmental patterns with spatial organization and molecular similarity to that of early embryonic stages. This self-organization of ESCs requires transmission of signaling cues, via addition of small molecule chemicals or recombinant proteins, to induce distinct embryonic cellular fates and subsequent assembly into structures that can mimic aspects of early embryonic development. During natural embryonic development, different embryonic cell types co-develop together, where each cell type expresses specific fate-inducing transcription factors through activation of non-coding regulatory elements and interactions with neighboring cells. However, previous studies have not fully explored the possibility of engineering endogenous regulatory elements to shape self-organization of ESCs into spatially-ordered embryo models. Here, we hypothesized that cell-intrinsic activation of a minimum number of such endogenous regulatory elements is sufficient to self-organize ESCs into early embryonic models. Our results show that CRISPR-based activation (CRISPRa) of only two endogenous regulatory elements in the genome of pluripotent stem cells is sufficient to generate embryonic patterns that show spatial and molecular resemblance to that of pre-gastrulation mouse embryonic development. Quantitative single-cell live fluorescent imaging showed that the emergence of spatially-ordered embryonic patterns happens through the intrinsic induction of cell fate that leads to an orchestrated collective cellular motion. Based on these results, we propose a straightforward approach to efficiently form 3D embryo models through intrinsic CRISPRa-based epigenome editing and independent of external signaling cues. CRISPRa-Programmed Embryo Models (CPEMs) show highly consistent composition of major embryonic cell types that are spatially-organized, with nearly 80% of the structures forming an embryonic cavity. Single cell transcriptomics confirmed the presence of main embryonic cell types in CPEMs with transcriptional similarity to pre-gastrulation mouse embryos and revealed novel signaling communication links between different embryonic cell types. Our findings offer a programmable embryo model and demonstrate that minimum intrinsic epigenome editing is sufficient to self-organize ESCs into highly consistent pre-gastrulation embryo models.
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Project description:Understanding the 3D genome organization in the nucleus is becoming increasingly crucial given its involvement in many processes from transcription to the integrity of the nucleus itself, which play a role in every stage of an organism's life. Beyond the linear genome defined by its nucleotide sequence, this organization is also governed by its epigenome, but how the latter controls the 3D architecture of the nucleus is poorly understood. To decipher the epigenome influence on the formation of all levels of the nuclear organization, we studied tomato mutants defective for DDM1, a chromatin remodeler determining for the constitutive heterochromatin establishment. We observed that the ddm1 mutant exhibited weakened compartmentalization with lower insulation, more inter-compartment contacts and an increase in long-range contacts. This disorganization is accompanied by a reconfiguration of the epigenome, ultimately resulting in a reprogramming of its transcriptome. By integrating all our data, we have shown that this redistribution of the epigenome is linked to the global disorganization of the nucleus notably via new interactions mediated by H3K27me3, and is also related to new interactions between genes and/or TEs which display the same epigenetic characteristics. Altogether, our results strongly suggest that epigenetic features drive the formation of distinct compartments by playing a segregating role between active and inactive chromatin, becoming an essential characteristic for the identity of genes and TEs in terms of genome organization.
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