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The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [RNA-seq]

ABSTRACT: The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [RNA-seq]

PROVIDER: PRJNA633800 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11811269_1.fastq.gz	Fastqsanger.gz
	SRR11811269_2.fastq.gz	Fastqsanger.gz
	SRR11811270_1.fastq.gz	Fastqsanger.gz
	SRR11811270_2.fastq.gz	Fastqsanger.gz
	SRR11811271_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [MNase-Seq]

Project description:The large family of ATP-dependent chromatin remodelers that regulate chromatin organization and composition are thought to act only on individual mononucleosomes. We discovered however that the yeast ISW1a remodeler has a much higher affinity for dinucleosomes and only efficiently converts ATP hydrolysis into nucleosome movement when bound to dinucleosomes, not mononucleosomes. The Ioc3 accessory subunit and its HLB DNA binding domain confer dinucleosome specificity onto the Isw1 catalytic subunit. Perturbation of ISW1a dinucleosome specificity by mutating Ioc3 interferes with its localization immediately downstream of the early transcription complex. ISW1a and NuA4, a histone acetyl transferase, and SWR1, a histone exchanger, are required together to slow early passage of RNA polymerase II. These findings provide new insights into the unusual specificity of a chromatin remodeler regulating the transition from transcription initiation to elongation and its functional interplay with other chromatin modifiers.

2020-07-31 | GSE150827 | GEO

The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [ChIP-seq]

2020-07-31 | GSE150826 | GEO

The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [RNA-seq]

2020-07-31 | GSE150828 | GEO

The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription

Project description:The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription

| PRJNA633796 | ENA

The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [MNase-Seq]

Project description:The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [MNase-Seq]

| PRJNA633799 | ENA

The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [ChIP-seq]

Project description:The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [ChIP-seq]

| PRJNA633798 | ENA

The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription

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

2020-07-31 | GSE150829 | GEO

The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells

Project description:Nucleosome remodeling factors regulate the occupancy and positioning of nucleosomes genome-wide through ATP-driven DNA translocation. While many nucleosomes are well- and consistently positioned, some nucleosomes and nucleosome-like structures are more sensitive to nuclease digestion or transitory in nature. To better understand the role of nucleosome remodeling factors in generating and clearing these alternative nucleosome structures, we depleted murine embryonic stem cells of the remodeler ATPases BRG1 and SNF2H then performed MNase-seq in murine embryonic stem cells. We performed MNase-seq under high- and low-MNase conditions to assess the effects of nucleosome remodeling factors on nuclease-sensitive or “fragile” nucleosome occupancy. In parallel, we gel-extracted MNase-digested fragments to enrich for another alternative nucleosome structure, the overlapping dinucleosome. Overlapping dinucleosomes are composed of two canonical nucleosomes, asymmetrically lacking one H2A:H2B dimer and wrapped by ~250 bp of DNA. In vitro studies of nucleosome remodeling have suggested that the collision of adjacent nucleosomes by nucleosome sliding can stimulate formation of overlapping dinucleosomes. Using these methods, we were able to identify fragile nucleosomes and overlapping dinucleosomes near transcription start sites and gene-distal DNaseI hypersensitive sites in mouse embryonic stem cells, among other loci. We find that BRG1 consistently stimulates occupancy of fragile nucleosomes but represses occupancy of overlapping dinucleosomes through its nucleosome remodeling function, while SNF2H expression slightly increases fragile nucleosome occupancy.

2023-03-14 | GSE216057 | GEO

Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation.

Project description:Over the last 3 decades ATP-dependent chromatin remodelers have been thought to recognize chromatin at the level of single nucleosomes rather than higher-order organization of more than one nucleosome. We show the yeast ISW1a remodeler has such higher-order structural specificity, as manifested by large allosteric changes that activate the nucleosome remodeling and spacing activities of ISW1a when bound to dinucleosomes. Although the ATPase domain of Isw1 docks at the SHL2 position when ISW1a is bound to either mono- or di-nucleosomes, there are major differences in the interactions of the catalytic subunit Isw1 with the acidic pocket of nucleosomes and the accessory subunit Ioc3 with nucleosomal DNA. By mutational analysis and uncoupling of ISW1a's dinucleosome specificity, we find that dinucleosome recognition is required by ISW1a for proper chromatin organization at promoters; as well as transcription regulation in combination with the histone acetyltransferase NuA4 and histone H2A.Z exchanger SWR1.

| S-EPMC7680125 | biostudies-literature

Structure of the ISW1a complex bound to the dinucleosome

Project description:Nucleosomes are basic repeating units of chromatin, and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes, and are vital in regulating chromatin organization and gene expression. Here we report the cryoEM structure of chromatin remodeler ISW1a complex bound to the dinucleosome. Each subunit of the complex recognizes a different nucleosome. The motor subunit binds to the mobile nucleosome and recognizes the acidic patch through two arginine residues, and the DNA-binding module interacts with the entry DNA at the nucleosome edge. This nucleosome-binding mode provides the structural basis for linker DNA sensing of the motor. Notably, the Ioc3 subunit recognizes the disk face of the adjacent nucleosome through interacting with the H4 tail, the acidic patch and the nucleosomal DNA, which plays a role in the spacing activity in vitro, and in nucleosome organization and cell fitness in vivo. Together, these findings support the nucleosome spacing activity of ISW1a, and add a new mode of nucleosome remodeling in the context of a chromatin environment.

2023-08-09 | GSE240192 | GEO

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