Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler

ABSTRACT: Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler

PROVIDER: PRJNA813226 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18250300_subreads.fastq.gz	Fastqsanger.gz
	SRR18250400_subreads.fastq.gz	Fastqsanger.gz
	SRR18250301_subreads.fastq.gz	Fastqsanger.gz
	SRR18250401_subreads.fastq.gz	Fastqsanger.gz
	SRR18250302_subreads.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 235

Similar Datasets

Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler

Project description:SAMOSA, a method previously developed in the Ramani Lab, was employed to reveal nucleosome patterns from remodeling reactions in vitro with the Imitation Switch (ISWI) ATP-Dependent Remodeler ATPase, SNF2h. SAMOSA was further employed to reveal single-molecule nucleosome patterns in vivo from SNF2h knockout and re-expression murine embryonic stem cells.

2023-08-03 | GSE197979 | GEO

Nucleosome recognition and DNA distortion by the Chd1 remodeler revealed at 2.6 Å resolution

Project description:Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. The Chd1 remodeler specializes in shifting nucleosomes into evenly spaced arrays, a defining characteristic of chromatin in gene bodies that blocks spurious transcription initiation. Linked to some forms of autism and commonly mutated in prostate cancer, Chd1 is essential for maintaining pluripotency in stem cells. Here we report a complex of yeast Chd1 bound to a nucleosome in a nucleotide-free state, determined by cryo-electron microscopy (cryo-EM) to 2.6 Å resolution. The structure shows a bulge of the DNA tracking strand where the ATPase motor engages the nucleosome, consistent with an initial stage in DNA translocation. Unlike other remodeler-nucleosome complexes, nucleosomal DNA compensates for the remodeler-induced bulge with a bulge of the complementary DNA strand one helical turn downstream from the ATPase motor. Unexpectedly, the structure also reveals an N-terminal binding motif, called ChEx, which binds on the exit-side acidic patch of the nucleosome. The ChEx motif can displace a LANA-based peptide from the acidic patch, which suggests a means by which Chd1 remodelers may block competing chromatin remodelers from acting on the opposite side of the nucleosome.

2022-02-23 | PXD025287 | Pride

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

Role of Itc1 subnit in ISW2 remodeler in nucleosome positioning and spacing in Saccharomyces cerevisiae

Project description:Role of Itc1 subnit in ISW2 remodeler in nucleosome positioning and spacing in Saccharomyces cerevisiae

2024-04-07 | GSE205956 | GEO

The Mi-2 nucleosome remodeler and the Rpd3 histone deacetylase are involved in piRNA-guided heterochromatin formation

Project description:In eukaryotes, trimethylation of lysine 9 on histone H3 (H3K9) is associated with transcriptional silencing of transposable elements (TEs). In drosophila ovaries, this heterochromatic repressive mark is thought to be deposited by SetDB1 on TE genomic loci after the initial recognition of nascent transcripts by PIWI-interacting RNAs (piRNAs) loaded on the Piwi protein. Here, we show that the nucleosome remodeler Mi-2, in complex with its partner MEP-1, forms a subunit that is transiently associated, in a MEP-1 C-terminus-dependent manner, with known Piwi interactors, including a recently reported SUMO ligase Su(var)2-10. Together with the histone deacetylase Rpd3, this module is involved in the piRNA-dependent TE silencing, correlated with H3K9 deacetylation and trimethylation. Therefore. drosophila piRNA-mediated transcriptional silencing involves three epigenetic effectors, a remodeler, Mi-2, an eraser, Rpd3 and a writer, SetDB1, in addition to the Su(var)2-10 SUMO ligase.

2020-07-21 | PXD018749 | Pride

Nucleosome intermediate preference of SMARCAD1 chromatin remodeler, and the structural insights

Project description:Nucleosome intermediate preference of SMARCAD1 chromatin remodeler, and the structural insights

| PRJNA1033990 | ENA

Nucleosome Positioning by an Evolutionarily Conserved Chromatin Remodeler Prevents Aberrant DNA Methylation in Neurospora.

Project description:Aberrant DNA methylation is often associated with cancers and DNA-demethylating agents such as 5-azacytidine (5-azaC) are often used for anti-tumor therapy. Although it is clinically effective at inhibiting DNA methylation, the mechanistic effect that 5-azaC elicits on eukaryotic cells is controversial. It has been proposed that incorporation of 5-azaC into DNA during replication irreversibly tethers cytosine methyltransferases (MTases) to DNA. This DNA-MTase adduct is targeted by the DNA repair machinery and removed to restore normal DNA functionality; as such some DNA repair mutants are sensitive to 5-azaC. However, double mutants lacking both the cytosine MTase and DNA repair enzymes are still 5-azaC susceptible. Here, we characterize a defective in methylation (dim) mutant of Neurospora crassa, dim-1, that is resistant to 5-azaC when DNA repair is abolished. The causative mutation in a dim-1 strain is in an AAA-ATPase chromatin remodeler conserved from yeast to humans, and indeed a Δdim-1 strain has atypically-spaced nucleosomes within heterochromatic, intergenic, and genic regions, suggesting that DIM-1 influences nucleosome positioning genome-wide. A dim-1 mutant has an ~40-50% reduction in total cytosine methylation but surprisingly gains new cytosine methylation peaks at intergenic regions that are often the promoters of highly expressed genes; nucleosome disorder and DIM-1 localization are also observed at these regions. We propose aberrant nucleosome density not only signals for the catalysis of cytosine methylation in Neurospora, but plays a role in 5-azaC resistance upon loss of DNA repair. Our data shed light on a new relationship between aberrant DNA methylation, DNA repair, an anti-tumor DNA demethylating agent, and nucleosome positioning.

2019-01-16 | GSE98911 | GEO

Nucleosome sliding by the Chd1 chromatin remodeler relies on the integrity of the DNA duplex

Project description:The experiments are done with three libraries by introducing base-pair perturbations on Widom 601: (1) poly(dA:dT) tract library (2) mismatch library (3) insertion library. And additional two more libraries based on native yeast genomic sequences: (4) Park97 mismatch library (5) Park97 insertion library. And we measured the nucleosome positioining in the base-pair resolution for before and after sliding by Chd1 chromatin remodeler.

2022-05-12 | GSE198440 | GEO

Sequence-Targeted Nucleosome Sliding in vivo - Nucleosome Mapping

Project description:Nucleosome positions were determined in wild type cells, cells lacking Isw2 or Ume6, and cells containing a hybrid Chd1-Ume6 chimeric remodeler

2016-03-12 | GSE72570 | GEO

Sequence-Targeted Nucleosome Sliding in vivo - Nucleosome Mapping

Project description:Nucleosome positions were determined in wild type cells, cells lacking Isw2 or Ume6, and cells containing a hybrid Chd1-Ume6 chimeric remodeler Matched MNase digests from W303 strain variants during log growth (OD600=0.4-0.6) were subject to paired-end sequencing for nucleosome mapping. For effects of the engineered fusion remodeling protein, a catalytically inactive (ATPase dead D513N) variant was included as a control.

2016-03-12 | E-GEOD-72570 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data