Modular regulation of Myc transcription by a topologically defined enhancer cluster dedicated to pluripotency and early embryonic expression
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE222299 | GEO | 2024/03/06
REPOSITORIES: GEO
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Project description:The transcription factor MYC plays essential roles in pluripotent stem cells, including the promotion of somatic cell reprogramming to pluripotency and the regulation of cell competition and embryonic diapause; however, how Myc expression is regulated in this context remains unknown. The Myc gene lies within a ~3-megabase gene desert that contains multiple cisregulatory elements. We used large-scale genomic deletions/inversions, BAC transgenesis and nested deletion of regulatory regions to characterize the cis-regulation of Myc transcription in the early mouse embryo and Embryonic Stem Cells (ESCs). We identified an Early Embryonic Expression (EEE) topologically-associated region that homes enhancers dedicated to Myc transcriptional regulation in stem cells of the early embryo, including the pluripotent cells of the inner cell mass, pre-implantation and post-implantation epiblast and other early embryonic stem cell populations. Within this region, we identified elements exclusively dedicated to Myc regulation in pluripotent cells, with distinct enhancers that sequentially regulate Myc ranscription during naive and formative pluripotency. Deletion of these pluripotency-specific enhancers dampens the competitive ability of ESCs. These results identify a topologically defined enhancer cluster dedicated to early embryonic expression and uncover a modular mechanism for the regulation of Myc expression in different states of pluripotency.
2024-03-06 | GSE222297 | GEO
Project description:The transcription factor MYC plays essential roles in pluripotent stem cells, including the promotion of somatic cell reprogramming to pluripotency and the regulation of cell competition and embryonic diapause; however, how Myc expression is regulated in this context remains unknown. The Myc gene lies within a ~3-megabase gene desert that contains multiple cisregulatory elements. We used large-scale genomic deletions/inversions, BAC transgenesis and nested deletion of regulatory regions to characterize the cis-regulation of Myc transcription in the early mouse embryo and Embryonic Stem Cells (ESCs). We identified an Early Embryonic Expression (EEE) topologically-associated region that homes enhancers dedicated to Myc transcriptional regulation in stem cells of the early embryo, including the pluripotent cells of the inner cell mass, pre-implantation and post-implantation epiblast and other early embryonic stem cell populations. Within this region, we identified elements exclusively dedicated to Myc regulation in pluripotent cells, with distinct enhancers that sequentially regulate Myc ranscription during naive and formative pluripotency. Deletion of these pluripotency-specific enhancers dampens the competitive ability of ESCs. These results identify a topologically defined enhancer cluster dedicated to early embryonic expression and uncover a modular mechanism for the regulation of Myc expression in different states of pluripotency.
2024-03-06 | GSE222294 | GEO
Project description:Modular regulation of Myc transcription by a topologically defined enhancer cluster dedicated to pluripotency and early embryonic expression
| PRJNA919171 | ENA
Project description:Modular regulation of Myc transcription by a topologically defined enhancer cluster dedicated to pluripotency and early embryonic expression [WGS]
| PRJNA919187 | ENA
Project description:Modular regulation of Myc transcription by a topologically defined enhancer cluster dedicated to pluripotency and early embryonic expression [4C-seq]
| PRJNA919185 | ENA
Project description:Embryonic stem cells (ESCs) are unique in that they have the capacity to differentiate into all of the cell types in the body. We know a lot about the complex transcriptional control circuits that maintain the naive pluripotent state under self-renewing conditions but comparatively less about how cells exit from this state in response to differentiation stimuli. Here, we examined the role of Otx2 in this process in mouse ESCs and demonstrate that it plays a leading role in remodeling the gene regulatory networks as cells exit from ground state pluripotency. Otx2 drives enhancer activation through affecting chromatin marks and the activity of associated genes. Mechanistically, Oct4 is required for Otx2 expression, and reciprocally, Otx2 is required for efficient Oct4 recruitment to many enhancer regions. Therefore, the Oct4-Otx2 regulatory axis actively establishes a new regulatory chromatin landscape during the early events that accompany exit from ground state pluripotency.
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Project description:While endogenous Myc (c-myc) and Mycn (N-myc) have been reported to be separately dispensable for murine embryonic stem cell (mESC) function, myc greatly enhances induced pluripotent stem (iPS) cell formation and overexpressed c-myc confers LIF-independence upon mESC. To address the role of myc genes in ESC and in pluripotency generally, we conditionally knocked out both c- and N-myc using myc doubly homozygously floxed mESC lines (cDKO). Both lines of myc cDKO mESC exhibited severely disrupted self-renewal, pluripotency, and survival along with enhanced differentiation. Chimeric embryos injected with DKO mESC most often completely failed to develop or in rare cases survived but with severe defects. The essential nature of myc for self-renewal and pluripotency is at least in part mediated through orchestrating pluripotency-related cell cycle and metabolic programs. This study demonstrates that endogenous myc genes are essential for mESC pluripotency and self-renewal as well as providing the first evidence that myc genes are required for early embryogenesis, suggesting potential mechanisms of myc contribution to iPS cell formation.
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Project description:Human embryonic stem cells (hESCs) depend on glycolysis for energy and substrates for biosynthesis. To understand the mechanisms governing the metabolism of hESCs, we investigated the transcriptional regulation of glucose transporter 1 (GLUT1, SLC2A1), a key glycolytic gene to maintain pluripotency. By combining the genome-wide data of binding sites of the core pluripotency factors (SOX2, OCT4, NANOG, denoted SON), chromosomal interaction and histone modification in hESCs, we identified a potential enhancer of the GLUT1 gene in hESCs, denoted GLUT1 enhancer (GE) element. GE interacts with the promoter of GLUT1, and the deletion of GE significantly reduces the expression of GLUT1, glucose uptake and glycolysis of hESCs, confirming that GE is an enhancer of GLUT1 in hESCs. In addition, the mutation of SON binding motifs within GE reduced the expression of GLUT1 as well as the interaction between GE and GLUT1 promoter, indicating that the binding of SON to GE is important for its activity. Therefore, SON promotes glucose uptake and glycolysis in hESCs by inducing GLUT1 expression through directly activating the enhancer of GLUT1.
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Project description:The Sox2 transcription factor must be robustly transcribed in embryonic stem (ES) cells to maintain pluripotency. Two gene-proximal enhancers, Sox2 regulatory region 1 (SRR1) and SRR2, display activity in reporter assays, but deleting SRR1 has no effect on pluripotency. We identified and functionally validated the sequences required for Sox2 transcription based on a computational model that predicted transcriptional enhancer elements within 130 kb of Sox2. Our reporter assays revealed three novel enhancers--SRR18, SRR107, and SRR111--that, through the formation of chromatin loops, form a chromatin complex with the Sox2 promoter in ES cells. Using the CRISPR/Cas9 system and F1 ES cells (Mus musculus(129) × Mus castaneus), we generated heterozygous deletions of each enhancer region, revealing that only the distal cluster containing SRR107 and SRR111, located >100 kb downstream from Sox2, is required for cis-regulation of Sox2 in ES cells. Furthermore, homozygous deletion of this distal Sox2 control region (SCR) caused significant reduction in Sox2 mRNA and protein levels, loss of ES cell colony morphology, genome-wide changes in gene expression, and impaired neuroectodermal formation upon spontaneous differentiation to embryoid bodies. Together, these data identify a distal control region essential for Sox2 transcription in ES cells.
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Project description:We examined the allelic expression and positioning of two pluripotency-associated genes, OCT4 and SOX2, and two housekeeping genes, ACTB and TUBA, in 4- and 8-cell porcine embryos utilizing RNA and DNA fluorescence in situ hybridization (FISH) in single blastomeres. The proportion of blastomeres expressing SOX2 bi-allelically increased from 45% at the 4-cell stage to 60% at the 8-cell stage. Moreover, in 8-cell embryos, SOX2 was expressed bi-allelically in significantly more blastomeres than was the case for OCT4, and this was associated with a tendency for SOX2 alleles to move toward the nuclear interior during 4- to 8-cell transition. However, the radial location of OCT4 alleles did not change significantly during this transition. The locations of active and inactive alleles based on DNA and RNA FISH signals were also calculated. Inactive OCT4 alleles were located in very close proximity to the nuclear membrane, whereas active OCT4 alleles were more centrally disposed in the nucleus. Nevertheless, the nuclear location of active and inactive SOX2 alleles did not change in either 4- or 8-cell blastomeres. Our RNA and DNA FISH data provide novel information on the allelic expression patterns and positioning of pluripotency-associated genes, OCT4 and SOX2, during embryonic genome activation in pigs.
| S-EPMC7378944 | biostudies-literature