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Relationship between nucleosome positioning and DNA methylation: Bisulfite-Seq, ChIP-Seq, and Mnase-Seq

ABSTRACT: Relationship between nucleosome positioning and DNA methylation: Bisulfite-Seq, ChIP-Seq, and Mnase-Seq

OTHER RELATED OMICS DATASETS IN: GSE21673

PROVIDER: PRJNA129325 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR052357.fastq.gz	Fastqsanger.gz
	SRR052358.fastq.gz	Fastqsanger.gz
	SRR052359.fastq.gz	Fastqsanger.gz
	SRR052360.fastq.gz	Fastqsanger.gz
	SRR052361.fastq.gz	Fastqsanger.gz

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Relationship between nucleosome positioning and DNA methylation: Bisulfite-Seq, ChIP-Seq, and Mnase-Seq

Project description:Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana utilizing massively parallel sequencing of mononucleosomes. By combining this data with profiles of DNA methylation at single base resolution, we identified ten base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA. These results suggest that nucleosome positioning strongly influences DNA methylation patterning throughout the genome and that DNA methyltransferases preferentially target nucleosome-bound DNA. We also observed similar trends in human nucleosomal DNA suggesting that the relationships between nucleosomes and DNA methyltransferases are conserved. Finally, as has been observed in animals, nucleosomes were highly enriched on exons, and preferentially positioned at intron-exon and exon-intron boundaries. RNA Pol II was also enriched on exons relative to introns, consistent with the hypothesis that nucleosome positioning regulates Pol II processivity. We also found that DNA methylation enriched on exons, consistent with the targeting of DNA methylation to nucleosomes. Genomic DNA from Arabidopsis thaliana was MNase digested, size selected and sequenced. Genomic DNA associated with H3 was isolated using ChIP and sequenced. Genomic DNA from human HSF1 embryonic stem cells was bisulfite converted and sequenced.

2010-05-29 | E-GEOD-21821 | biostudies-arrayexpress

Regulation of nucleosome positioning by a CHD Type III chromatin remodeller and its relationship to developmental gene expression in Dictyostelium [MNase-seq]

Project description:We utilized MNase-seq to profile nucleosome positions in wild type (Ax2) and ChdC null cells both in growing cells and a partially developed state (loose-mound) to study changes in nucleosome positioning and occupancy during development and the impact the deletion of ChdC an ATP-dependent chromatin remodeller has on nucleosome positioning and occupancy. As a control for MNase sequence bias we also digested naked DNA with MNase.

2017-02-26 | GSE70122 | GEO

Relationship between nucleosome positioning and DNA methylation: Bisulfite-Seq, ChIP-Seq, and Mnase-Seq

2010-05-29 | GSE21821 | GEO

E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning [MNase-Seq]

Project description:E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning [MNase-Seq]

| PRJNA507858 | ENA

Genome-wide nucleosome positioning during embryonic stem cell development

Project description:This SuperSeries is composed of the following subset Series: GSE40910: Genome-wide nucleosome positioning during embryonic stem cell development [MNase-Seq] GSE40948: Genome-wide nucleosome positioning during embryonic stem cell development [RNA-Seq] GSE40951: Genome-wide nucleosome positioning during embryonic stem cell development [ChIP-Seq] Refer to individual Series

2012-10-21 | E-GEOD-40896 | biostudies-arrayexpress

Nucleosome positioning study of Arabidopsis er/erl1/erl2 mutant using MNase-seq approach

Project description:Nucleosome positioning study of Arabidopsis er/erl1/erl2 mutant using MNase-seq approach

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MNase-seq facilitates quantitative analysis of nucleosome positioning of wild type and mutant SWI/SNF complexes

Project description:Purpose: The goal of this study is to evaluate potentially direct targets of altered chromatin remodeller SWI/SNF on nucleosome positioning at gene promoters by means of MNase-sequencing from synchronised L1-staged swsn‑1 single mutant, swsn‑1; snfc‑5 double mutants, swsn‑1; snfc‑5; ubr‑5 triple mutants compared to wild-type animals to achieve genome-wide nucleosome coverage profiles. Methods: In vivo MNAse-seq profiles of WT (N2), swsn-1-/- (MH2354, SX3714), swsn-1-/-; snfc-5-/- (SX3622, SX3715), swsn-1-/-; snfc-5-/-; ubr-5-/- (SX3627) C. elegans L1s were generated by deep sequencing, in duplicate, using Illumina NextSeq 2000. The sequence reads that passed quality filters were mapped to C. elegans (ce11) genome using bowtie2 aligner v.2.2.9. The resulting bam files were converted to bigwig tracks using deeptools bamCoverage. Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the C elegans genome (build ce11). MNase-Seq data was further analysed locus-by-locus for nucleosome positioning around transcription start site of ubiquitous genes in the mutants relative to wild-type coverage. Swsn-1 single mutants showed strongly reduced +1 nucleosome coverage in compare to the wild-type animals. The +1-nucleosome coverage in both the swsn-1; snfc-5 double and swsn-1; snfc-5; ubr-5 triple suppressor mutants was higher than in swsn-1 single mutants. We also established that the subsets of ubiquitously up and downregulated SWI/SNF-dependent genes have a higher nucleosome coverage in wild-type animals when compared to all ubiquitous genes in wild-type animals.

2023-01-01 | GSE218808 | GEO

SMARCAD1 Regulates Nucleosome Positioning and Maintenance of the Naïve Pluripotent State

Project description:Genome-wide maps of nucleosome positioning in mouse ES cells with control shRNA and on Smarcad1 KD. MNase-seq data for human colo829 cells are also included.

2014-12-30 | GSE47802 | GEO

Promoter nucleosome positioning in dendritic cells (DCs) and fibroblasts measured by ChIP-MNase-seq

Project description:Promoter nucleosome positioning in dendritic cells (DCs) and fibroblasts measured by ChIP-MNase-seq

| PRJNA596344 | ENA

PING 2.0: An R/Bioconductor package for nucleosome positioning using next-generation sequencing data

Project description:MNase-Seq and ChIP-Seq have evolved as popular techniques to study chromatin and histone modification. Although many tools have been developed to identify enriched regions, software tools for nucleosome positioning are still limited. We introduce a flexible and powerful open-source R package, PING 2.0, for nucleosome positioning using MNase-Seq data or MNase- or sonicated- ChIP-Seq data combined with either single-end or paired-end sequencing. PING uses a model-based approach, which enables nucleosome predictions even in the presence of low read counts. We illustrate PING using two paired-end datasets from Saccharomyces cerevisiae and compare its performance to nucleR and ChIPseqR.

2013-07-11 | GSE47073 | GEO

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