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Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation [HiChIP]

ABSTRACT: Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation [HiChIP]

PROVIDER: PRJNA833451 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18976877_1.fastq.gz	Fastqsanger.gz
	SRR18976877_2.fastq.gz	Fastqsanger.gz
	SRR18976878_1.fastq.gz	Fastqsanger.gz
	SRR18976878_2.fastq.gz	Fastqsanger.gz
	SRR18976879_1.fastq.gz	Fastqsanger.gz

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Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation

Project description:Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation

| PRJNA844097 | ENA

Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation [HiChIP]

Project description:Background: CTCF is a well-established chromatin architectural protein that also plays various roles in transcriptional regulation. While CTCF biology has been extensively studied, how the domains of CTCF function to regulate transcription remains unknown. Additionally, the original auxin-inducible degron 1 (AID1) system has limitations to investigate the function of CTCF. Results: We employ an improved auxin-inducible degron technology, AID2, to facilitate the study of acute depletion of CTCF while overcoming the limitations of the previous AID system. As previously observed through the AID1 system and steady-state RNA analysis, the new AID2 system combined with SLAM-seq confirms that CTCF depletion leads to modest nascent and steady-state transcripts changes. A CTCF domain sgRNA library screening identifies the zinc finger (ZF) domain as the region within CTCF with the most functional relevance, including ZFs 1 and 10. Removal of ZFs 1 and 10 reveals genomic regions that independently require these ZFs for DNA binding and transcriptional regulation. Notably, loci regulated by either ZF1 or ZF10 exhibit unique CTCF binding motifs specific to each ZF. Conclusions: By extensively comparing the AID1 and AID2 systems for CTCF degradation in SEM cells, we confirm that AID2 degradation is superior for achieving miniAID tagged protein degradation without the limitations of the AID1 system. The model we create that combines AID2 depletion of CTCF with exogenous overexpression of CTCF mutants allows us to demonstrate how peripheral ZFs intricately orchestrate transcriptional regulation in a cellular context for the first time.

2022-12-09 | GSE201911 | GEO

Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation [RNA-Seq]

Project description:Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation [RNA-Seq]

| PRJNA844363 | ENA

Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation [SLAM-seq]

Project description:Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation [SLAM-seq]

| PRJNA844055 | ENA

Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation [RNA-Seq]

2022-12-09 | GSE205311 | GEO

Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation [SLAM-seq]

2022-12-09 | GSE205184 | GEO

Advanced auxin-inducible degron system deciphers unique functions of CTCF in transcriptional regulation [ChIP-seq]

Project description:Advanced auxin-inducible degron system deciphers unique functions of CTCF in transcriptional regulation [ChIP-seq]

| PRJNA844978 | ENA

Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation.

Project description:BackgroundCTCF is a well-established chromatin architectural protein that also plays various roles in transcriptional regulation. While CTCF biology has been extensively studied, how the domains of CTCF function to regulate transcription remains unknown. Additionally, the original auxin-inducible degron 1 (AID1) system has limitations in investigating the function of CTCF.ResultsWe employ an improved auxin-inducible degron technology, AID2, to facilitate the study of acute depletion of CTCF while overcoming the limitations of the previous AID system. As previously observed through the AID1 system and steady-state RNA analysis, the new AID2 system combined with SLAM-seq confirms that CTCF depletion leads to modest nascent and steady-state transcript changes. A CTCF domain sgRNA library screening identifies the zinc finger (ZF) domain as the region within CTCF with the most functional relevance, including ZFs 1 and 10. Removal of ZFs 1 and 10 reveals genomic regions that independently require these ZFs for DNA binding and transcriptional regulation. Notably, loci regulated by either ZF1 or ZF10 exhibit unique CTCF binding motifs specific to each ZF.ConclusionsBy extensively comparing the AID1 and AID2 systems for CTCF degradation in SEM cells, we confirm that AID2 degradation is superior for achieving miniAID-tagged protein degradation without the limitations of the AID1 system. The model we create that combines AID2 depletion of CTCF with exogenous overexpression of CTCF mutants allows us to demonstrate how peripheral ZFs intricately orchestrate transcriptional regulation in a cellular context for the first time.

| S-EPMC9878928 | biostudies-literature

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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