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The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development [FAIRE-seq]

ABSTRACT: The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development [FAIRE-seq]

PROVIDER: PRJNA1023553 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26266481_1.fastq.gz	Fastqsanger.gz
	SRR26266481_2.fastq.gz	Fastqsanger.gz
	SRR26266482_1.fastq.gz	Fastqsanger.gz
	SRR26266482_2.fastq.gz	Fastqsanger.gz
	SRR26266483_1.fastq.gz	Fastqsanger.gz

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The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development

Project description:The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development

| PRJNA1023544 | ENA

The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development [H3K27ac Cut & Run]

Project description:The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development [H3K27ac Cut & Run]

| PRJNA1023547 | ENA

The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development [anti-GFP Cut & Run]

Project description:The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development [anti-GFP Cut & Run]

| PRJNA1023549 | ENA

The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development [FAIRE-seq]

Project description:Chromatin remodeling is central to the dynamic changes in gene expression that drive cell fate determination. During development, the sets of enhancers that are accessible for use change globally as cells transition between stages. While transcription factors and nucleosome remodelers are known to work together to control enhancer accessibility, it is unclear how the short stretches of DNA that they individually unmask yield the kilobase-sized accessible regions characteristic of active enhancers. Here, we performed a genetic screen to investigate the role of nucleosome remodelers in control of dynamic enhancer activity. We find that the Drosophila SWI/SNF complex, BAP, is required for repression of a temporally dynamic enhancer, brdisc. Contrary to expectations, we find that the BAP-specific subunit Osa is dispensable for mediating changes in chromatin accessibility between early and late stages of wing development. Instead, we find that Osa is required to constrain the levels of brdisc activity when the enhancer is normally active. Genome-wide profiling reveals that Osa directly binds brdisc as well as thousands of other developmentally dynamic regulatory sites, including multiple genes encoding components and targets of the Notch signaling pathway. Transgenic reporter analyses demonstrate that Osa is required for activation and for constraint of different sets of target enhancers in the same cells. Moreover, Osa loss results in hyperactivation of the Notch ligand Delta and development of ectopic sensory structures patterned by Notch signaling early in development. Together, these findings indicate that proper constraint of enhancer activity is necessary for regulation of dose-dependent developmental events.

2023-10-03 | GSE244555 | GEO

The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development [H3K27ac Cut & Run]

2023-10-03 | GSE244552 | GEO

The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development [anti-GFP Cut & Run]

2023-10-03 | GSE244553 | GEO

The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development

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

2023-10-03 | GSE244556 | GEO

Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement

Project description:Eukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility. The Saccharomyces cerevisiae RSC (Remodeling the Structure of Chromatin) complex, a member of the SWI/SNF chromatin remodeler family, plays critical roles in genome maintenance, transcription, and DNA repair. Here, we report cryo-electron microscopy (cryo-EM) and crosslinking mass spectrometry (CLMS) studies of yeast RSC complex and show that RSC is composed of a rigid tripartite core and two flexible lobes. The core structure is scaffolded by an asymmetric Rsc8 dimer and built with the evolutionarily conserved subunits Sfh1, Rsc6, Rsc9 and Sth1. The flexible ATPase lobe, composed of helicase subunit Sth1, Arp7, Arp9 and Rtt102, is anchored to this core by the N-terminus of Sth1. Our cryo-EM analysis of RSC bound to a nucleosome core particle shows that in addition to the expected nucleosome-Sth1 interactions, RSC engages histones and nucleosomal DNA through one arm of the core structure, composed of the Rsc8 SWIRM domains, Sfh1 and Npl6. Our findings provide structural insights into the conserved assembly process for all members of the SWI/SNF family of remodelers, and illustrate how RSC selects, engages, and remodels nucleosomes.

2020-05-27 | PXD019400 | Pride

Nucleosome remodeler exclusion by histone deacetylation enforces heterochromatic silencing and epigenetic inheritance

Project description:Heterochromatin enforces transcriptional gene silencing and can be epigenetically inherited, but the underlying mechanism has remained unclear.Here we show that histone deacetylation, a conserved feature of heterochromatin domains, blocks SWI/SNF subfamily remodelers involved in chromatin unraveling, thereby stabilizing modified nucleosomes that preserve gene silencing. Histone hyperacetylation, resulting from either the loss of a histone deacetylase (HDAC) or the direct targeting of histone acetyltransferase to heterochromatin, permits remodeler access, leading to silencing defects.The requirement for HDAC in heterochromatin silencing can be bypassedby impeding SWI/SNF activity. Highlighting the crucial role of remodelers, merely targeting SWI/SNF to heterochromatin, even in cells with functional HDAC, increases nucleosome turnover, causing defective gene silencing and compromised epigenetic inheritance. This study elucidates a fundamental mechanism whereby histone hypoacetylation, maintained by high HDAC levels in heterochromatic regions, ensures stable gene silencing and epigenetic inheritance,providing significant insights into genome regulation relevant to human diseases.

2024-08-05 | GSE269243 | GEO

FAIRE-seq

Project description:FAIRE-seq

| PRJEB2459 | ENA