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Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening [scRNA-seq]

ABSTRACT: Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening [scRNA-seq]

PROVIDER: PRJNA517137 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8487461_1.fastq.gz	Fastqsanger.gz
	SRR8487461_2.fastq.gz	Fastqsanger.gz

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Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening [scRNA-seq]

Project description:Pioneer transcription factors are coined as having the unique property of “opening closed chromatin sites” for implementation of cell fates. We previously showed that the pioneer Pax7 specifies melanotrope cells through deployment of an enhancer repertoire: this allows binding of Tpit, a nonpioneer factor that determines the related lineages of melanotropes and corticotropes. Here, we investigated the relation between these two factors in the pioneer mechanism. Cell-specific gene expression and chromatin landscapes were defined by scRNAseq and chromatin accessibility profiling. We found that in vivo deployment of the melanotrope enhancer repertoire and chromatin opening requires both Pax7 and Tpit. In cells, binding of heterochromatin targets by Pax7 is independent of Tpit but Pax7-dependent chromatin opening requires Tpit. The present work shows that pioneer core properties are limited to the ability to recognize heterochromatin targets and facilitate nonpioneer binding. Chromatin opening per se may be provided through cooperation with nonpioneer factors.

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Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening

Project description:Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening

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Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening [ChIP-seq]

Project description:Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening [ChIP-seq]

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Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening.

Project description:Pioneer transcription factors are characterized by having the unique property of enabling the opening of closed chromatin sites, for implementation of cell fates. We previously found that the pioneer Pax7 specifies melanotrope cells through deployment of an enhancer repertoire, which allows binding of Tpit, a nonpioneer factor that determines the related lineages of melanotropes and corticotropes. Here, we investigate the relation between these two factors in the pioneer mechanism. Cell-specific gene expression and chromatin landscapes are defined by scRNAseq and chromatin accessibility profiling. We find that in vivo deployment of the melanotrope enhancer repertoire and chromatin opening requires both Pax7 and Tpit. In cells, binding of heterochromatin targets by Pax7 is independent of Tpit but Pax7-dependent chromatin opening requires Tpit. The present work shows that pioneer core properties are limited to the ability to recognize heterochromatin targets and facilitate nonpioneer binding. Chromatin opening per se may be provided through cooperation with nonpioneer factors.

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Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening

Project description:This SuperSeries is composed of the SubSeries listed below.

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Chromatin opening ability of pioneer factor Pax7 depends on unique isoform and C-terminal domain (RNA-Seq)

Project description:Pioneer factors are transcription factors (TFs) that have the unique ability to recognise their target DNA sequences within closed chromatin. Whereas their interactions with cognate DNA is similar to other TFs, their ability to interact with chromatin remains poorly understood. Having previously defined the modalities of DNA interactions for the pioneer factor Pax7, we have now used natural isoforms of this pioneer as well as deletion and replacement mutants to investigate the Pax7 structural requirements for chromatin interaction and opening. We show that the GL+ natural isoform of Pax7 that has two extra amino acids within the DNA binding paired domain is unable to activate the melanotrope transcriptome and to fully activate a large subset of melanotrope-specific enhancers targeted for Pax7 pioneer action. This enhancer subset remains in the primed state rather than being fully activated, despite the GL+ isoform having similar intrinsic transcriptional activity as the GL- isoform. C-terminal deletions of Pax7 lead to the same loss of pioneer ability, with similar reduced recruitments of the cooperating TF Tpit and of the co-regulators Ash2 and BRG1. This suggest complex interrelations between the DNA binding and C-terminal domains of Pax7 that are crucial for its chromatin opening pioneer ability.

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Chromatin opening ability of pioneer factor Pax7 depends on unique isoform and C-terminal domain (ChIP-Seq)

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