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Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [ChIP-seq I]

ABSTRACT: Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [ChIP-seq I]

PROVIDER: PRJNA792949 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17373825_1.fastq.gz	Fastqsanger.gz
	SRR17373825_2.fastq.gz	Fastqsanger.gz
	SRR17373826_1.fastq.gz	Fastqsanger.gz
	SRR17373826_2.fastq.gz	Fastqsanger.gz
	SRR17373827_1.fastq.gz	Fastqsanger.gz

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Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes

Project description:Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes

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Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [scATAC-seq]

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Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [scRNA-seq]

Project description:Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [scRNA-seq]

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Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [ChIP-seq II]

Project description:Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [ChIP-seq II]

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Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [RNA-seq III]

Project description:Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [RNA-seq III]

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Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [RNA-seq II]

Project description:Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [RNA-seq II]

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Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [RNA-seq I]

Project description:Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [RNA-seq I]

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Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [MA Timepoint RNA-seq]

Project description:Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [MA Timepoint RNA-seq]

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Cross-lineage potential of Ascl1 uncovered by comparing diverse reprogramming regulatomes.

Project description:Direct reprogramming has revolutionized the fields of stem cell biology and regenerative medicine. However, the common mechanisms governing how reprogramming cells undergo transcriptome and epigenome remodeling (i.e., regulatome remodeling) have not been investigated. Here, by characterizing early changes in the regulatome of three different types of direct reprogramming, we identify lineage-specific features as well as common regulatory transcription factors. Of particular interest, we discover that the neuronal factor Ascl1 possesses cross-lineage potential; together with Mef2c, it drives efficient cardiac reprogramming toward a mature and induced cardiomyocyte phenotype. Through ChIP-seq and RNA-seq, we find that MEF2C drives the shift in ASCL1 binding away from neuronal genes toward cardiac genes, guiding their co-operative epigenetic and transcription activities. Together, these findings demonstrate the existence of common regulators of different direct reprogramming and argue against the premise that transcription factors possess only lineage-specific capabilities for altering cell fate - the basic premise used to develop direct reprogramming approaches.

| S-EPMC9557912 | biostudies-literature

Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [scATAC-seq]

Project description:Direct reprogramming has revolutionized the fields of stem cell biology and regenerative medicine. Direct reprogramming makes it possible to interconvert somatic cell fates without intermediary pluripotency. Although studies have identified different transcription factor (TF) cocktails that can reprogram fibroblasts into different cell types, the common mechanisms governing how reprogramming cells undergo transcriptome and epigenome remodeling (i.e. regulatome remodeling) have not been investigated. Here, by characterizing early changes in the regulatome of three different types of direct reprogramming – induced neurons, induced hepatocytes, and induce cardiomyocytes – we identified two non-cocktail TFs, Tead4 and Atf7, that co-operate with reprogramming TFs to regulate target cell-type specific gene expression. Additionally, by identifying shared pro-cardiac features of iN and iCM reprogramming, we demonstrate Ascl1’s cross-lineage potential to induce highly efficient iCM reprogramming in a two-factor cocktail with Mef2c (A+M). Single-cell multi-omics showed that A+M reprogramming terminates in a more mature iCM phenotype than MGT. Finally, through ChIP-seq and RNA-seq, we find that Mef2c drives the shift in Ascl1 binding away from neuronal genes towards cardiac gene, guiding their co-operative epigenetic and transcription activities. These findings demonstrate the existence of common regulators of different direct reprogramming process and argue against the premise that TFs are lineage specific – the basic premise used to develop direct reprogramming approaches.

2022-09-15 | GSE192738 | GEO

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