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Auxin-degron system identifies immediate mechanisms of Oct4 [RNA-seq]

ABSTRACT: Auxin-degron system identifies immediate mechanisms of Oct4 [RNA-seq]

PROVIDER: PRJNA712292 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13918150_1.fastq.gz	Fastqsanger.gz
	SRR13918150_2.fastq.gz	Fastqsanger.gz
	SRR13918151_1.fastq.gz	Fastqsanger.gz
	SRR13918151_2.fastq.gz	Fastqsanger.gz
	SRR13918152_1.fastq.gz	Fastqsanger.gz

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Auxin-degron system identifies immediate mechanisms of Oct4

Project description:Auxin-degron system identifies immediate mechanisms of Oct4

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Auxin-degron system identifies immediate mechanisms of Oct4 [H3K27ac ChIP-seq]

Project description:Auxin-degron system identifies immediate mechanisms of Oct4 [H3K27ac ChIP-seq]

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Auxin-degron system identifies immediate mechanisms of Oct4 [Nanog ChIP-seq]

Project description:Auxin-degron system identifies immediate mechanisms of Oct4 [Nanog ChIP-seq]

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Auxin-degron system identifies immediate mechanisms of Oct4 [RNA-seq]

Project description:The pluripotency factor Oct4 is essential for the maintenance of naïve pluripotent stem cells in vitro and in vivo. However, the specific role of Oct4 in this process remains unknown. Here, we developed a rapid protein-level Oct4 depletion system that demonstrates that the immediate downstream response to loss of Oct4 is reduced expression of key pluripotency factors. Our data show a requirement for Oct4 for the efficient transcription of several key pluripotency factors, and suggest that expression of trophectoderm markers is a subsequent event. Additionally, we find that Nanog is competent to bind to the genome in the absence of Oct4, and this binding is in fact enhanced. Globally, however, active enhancer associated histone mark H3K27ac is depleted. Our work establishes that while Oct4 is required for the maintenance of the naïve transcription factor network, at a normal ESC level it antagonises this network through inhibition of Nanog binding

2021-06-17 | GSE168577 | GEO

Auxin-degron system identifies immediate mechanisms of Oct4 [H3K27ac ChIP-seq]

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Auxin-degron system identifies immediate mechanisms of Oct4 [Nanog ChIP-seq]

2021-06-17 | GSE168576 | GEO

Auxin-degron system identifies immediate mechanisms of OCT4.

Project description:The pluripotency factor OCT4 is essential for the maintenance of naive pluripotent stem cells in vitro and in vivo. However, the specific role of OCT4 in this process remains unknown. Here, we developed a rapid protein-level OCT4 depletion system that demonstrates that the immediate downstream response to loss of OCT4 is reduced expression of key pluripotency factors. Our data show a requirement for OCT4 for the efficient transcription of several key pluripotency factors and suggest that expression of trophectoderm markers is a subsequent event. In addition, we find that NANOG is able to bind to the genome in the absence of OCT4, and this binding is in fact enhanced. Globally, however, the active enhancer-associated histone mark H3K27ac is depleted. Our work establishes that, while OCT4 is required for the maintenance of the naive transcription factor network, at a normal embryonic stem cell levels it antagonizes this network through inhibition of NANOG binding.

| S-EPMC8282470 | biostudies-literature

Auxin-degron system identifies immediate mechanisms of Oct4

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

2021-06-17 | GSE168579 | GEO

Degron flexibility enforces auxin sensing

Project description:Cullin RING-type E3 ubiquitin ligase SCFTIR1/AFB1-5 and their ubiquitylation targets, AUX/IAAs, sense auxin concentrations in the nucleus. TIR1 binds a surface- exposed degron in AUX/IAAs promoting their ubiquitylation and rapid auxin-regulated proteasomal degradation. Here, we resolved TIR1·auxin·IAA7 and TIR1·auxin·IAA12 complex topology, and show that flexible intrinsically disordered regions (IDRs) cooperatively position AUX/IAAs on TIR1. The AUX/IAA PB1 interaction domain also assists in non-native contacts, affecting AUX/IAA dynamic interaction states. Our results establish a role for IDRs in modulating auxin receptor assemblies. By securing AUX/IAAs on two opposite surfaces of TIR1, IDR diversity supports locally tailored positioning for targeted ubiquitylation, and might provide conformational flexibility for adopting a multiplicity of functional states. We postulate IDRs in distinct members of the AUX/IAA family to be an adaptive signature for protein interaction and initiation region for proteasome recruitment.

2020-05-27 | PXD015392 | Pride

Transcriptomic analysis of the Xrn1 depletion by Auxin-degron shutoff

Project description:The goal of the project was to study the effects on transcription and mRNA stability of the Xrn1 sudden depletion. We analyzed the effect of Xrn1 depletion caused by protein degradation of an Auxin-degron fusion on the transcription rates, mRNA stabilities and mRNA levels by doing Genomic Run-On (GRO) experiments at 30 min after Auxin addition with a control at 0 min.

2019-02-22 | GSE123326 | GEO

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