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H3K4 Methylation-Mediated Memory of an Active Transcriptional State Impairs Nuclear Reprogramming

ABSTRACT: Xenopus eggs can induce the reversal of differentiation processes of somatic cells. Yet, the egg is not fully efficient in reprogramming a differentiated nucleus, as certain genes retain a memory of gene expression of their somatic cell of origin. This is thought to be a reason for the low success rate of current cloning and reprogramming strategies. While previous studies addressed extensively the mechanisms that maintain an inactive state of genes (OFF-memory), we investigated the importance of memory of an active transcriptional state (ON-memory) in maintaining cell fate identity and on resistance to reprogramming. We find that donor cell-type specific ON-memory gene-expression in the wrong cell-type of nuclear transfer (NT)-embryos is as common as OFF-memory gene-expression. When compared to properly reprogrammed genes, we find that ON-memory genes show an elevated level of the active histone mark H3K4me3 in endoderm donor cells. Importantly, we show that a reduction of H3K4 methylation level in donor cells decreases the extent of ON-memory gene expression, globally improves transcriptional reprogramming, and enhances the development of NT-embryos. Therefore, our study reveals that H3K4 methylation safeguards endoderm cell identity and acts as a major barrier for efficient reprogramming in NT-embryos. Furthermore, our results suggest that efficient cell fate reprogramming not only relies on the erasure of epigenetic modifications conferring OFF-memory but also crucially depends on the removal of H3 lysine 4 methylation-mediated memory of an active state of gene expression.

ORGANISM(S): Xenopus laevis

PROVIDER: GSE92366 | GEO | 2017/03/31

SECONDARY ACCESSION(S): PRJNA357356

REPOSITORIES: GEO

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Project description:Human pluripotent stem cells hold great potential for regenerative medicine, but available cell types have important limitations. While embryonic stem cells derived from fertilized embryos (IVF-ESCs) are considered the "gold standard" of pluripotency, they are allogeneic to potential recipients. Autologous induced pluripotent stem cells (iPSCs) are prone to epigenetic and transcriptional aberrations. To determine whether accumulation of such aberrations is intrinsic to somatic cell reprogramming or secondary to the reprogramming method, we generated a genetically matched collection of human IVF-ESCs, iPSCs, and ESCs derived by somatic cell nuclear transfer (SCNT; NT-ESCs), and subjected them to genome-wide genetic, epigenetic and transcriptional analyses. SCNT-based reprogramming is mediated by the full complement of oocyte cytoplasmic factors, thus closely recapitulating early embryogenesis. NT-ESCs and iPSCs derived from the same somatic donor cells contained comparable numbers of de novo copy number variations (CNVs), suggesting that the two reprogramming methods may not differ significantly in mutagenic or selective pressure. On the other hand, the DNA methylation and transcriptome profiles of NT-ESCs corresponded very closely to those of IVF-ESCs, while iPSCs differed markedly from IVF-ESCs and harbored residual DNA methylation patterns typical of parental fibroblasts, suggesting incomplete reprogramming. We conclude that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT and are therefore ideal candidates for cell replacement therapies. 16 matched samples, two IVF-ESCs, five sendai produced iPSC lines, two retro-virus produced iPSC lines, four NT-ESCs, the parental fibroblast line, and the sperm and oocyte donor were genotyped using the Illumina Omni5, which interrogates 4.3 million SNPs across the human genome. Additionally, matched samples from a patient with Leigh syndrome, a NT-ESC line, three iPSC lines, and the parental fibroblast line were genotyped using the Illumina Omni5.

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H3K4 Methylation-Mediated Memory of an Active Transcriptional State Impairs Nuclear Reprogramming

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