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Global DNA methylation remodeling during direct reprogramming from fibroblast to neuron [MethylC-seq]

ABSTRACT: Global DNA methylation remodeling during direct reprogramming from fibroblast to neuron [MethylC-seq]

PROVIDER: PRJNA436411 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6793540.fastq.gz	Fastqsanger.gz
	SRR6793550.fastq.gz	Fastqsanger.gz
	SRR6793560.fastq.gz	Fastqsanger.gz
	SRR6793541.fastq.gz	Fastqsanger.gz
	SRR6793551.fastq.gz	Fastqsanger.gz

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Global DNA methylation remodeling during direct reprogramming from fibroblast to neuron [MethylC-seq]

Project description:Direct reprogramming from fibroblasts to neurons induces widespread cellular and transcriptional reconfigurations. In this study, we characterized global epigenomic changes during direct reprogramming using whole-genome base-resolution DNA methylome (mC) sequencing. We found that the pioneer transcription factor Ascl1 alone is sufficient for inducing robust non-CG methylation (mCH) accumulation in reprogrammed cells, but co-expression of Brn2 and Mytl1 was required to establish a global mCH pattern reminiscent of mature cortical neurons. Ascl1 alone induced strong promoter CG methylation (mCG) of fibroblast specific genes, while BAM overexpression additionally targets a competing myogenic program and directs a more faithful conversion to neuronal cells. Ascl1 induces local demethylation at its binding sites. Surprisingly, co-expression with Brn2 and Mytl1 inhibited the ability of Ascl1 to induce demethylation, suggesting a contextual regulation of transcription factor - epigenome interaction. Finally, we found that de novo methylation by DNMT3A is required for efficient neuronal reprogramming.

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RNA-seq timeline of fibroblast to neuron conversion using traditional NC media and NC+ZPAK media

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Project description:Direct conversion from fibroblast to neuron has recently been successfully induced bypassing the pluripotent state. However, the conversion takes a few months with low percentages of success. Here we found that depletion of p53, which can converted fibroblasts into three major neural lineages: neurons, astrocytes and oligodendrocytes. Furthermore, our method provided a high efficiency of conversion in aging fibroblasts, where published methods failed. This finding may help developing a prototype for neuron replacement therapy, including foraging people vulnerable to neurological disorders. p53 has been shown to inhibit reprogramming of fibroblasts to iPS cells, by depletion of p53 in human fibroblasts, we study the function of p53 in induced neuron process. By induction of p53 knockdown fibroblasts with special neuron medium, we can get mature neurons directly. In the induction process, many neurogenic transcription factors were up-regulated, and we prove that p21 is not involved in this process.

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