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Nucleosome positioning dynamics during the cold-induced silencing of the Arabidopsis FLC gene using targeted MNase-seq

ABSTRACT: Nucleosome positioning dynamics during the cold-induced silencing of the Arabidopsis FLC gene using targeted MNase-seq

PROVIDER: PRJNA1144889 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30155932_1.fastq.gz	Fastqsanger.gz
	SRR30155932_2.fastq.gz	Fastqsanger.gz
	SRR30155933_1.fastq.gz	Fastqsanger.gz
	SRR30155933_2.fastq.gz	Fastqsanger.gz
	SRR30155934_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Nucleosome positioning dynamics during the cold-induced silencing of the Arabidopsis FLC gene using targeted MNase-seq

Project description:Micrococcal nuclease (MNase) has been extensively used to map nucleosomes genome wide. Here, we used a targeted MNase-seq approach to map nucleosomes at high resolution at the FLC locus during the cold-induced silencing. This strategy uncovered that the +1 nucleosome at FLC is repositioned closer to the promoter in response to cold. The nucleosome repositioning alters the chromatin structure locally at the 5’ end of FLC and is linked to the silencing of the gene. Moreover, this is in part modulated by VRN1, a non-sequence-specific DNA binding protein that associates with FLC promoter and is required for its silencing.

2025-05-07 | GSE274066 | GEO

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

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

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

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

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

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

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

Cold-induced silencing mediated by long antisense FLC transcripts

Project description:Hight throughput techniques have revealed huge complexity in antisense RNAs in many organisms. We have explored the complexity of this class of transcripts and functional links to Polycomb silencing thought analysis of non-coding RNAs of Arabidopsis FLC. FLC is repressed and epigenetically silenced by prolonged cold, enabling plants to undergo the floral transition. Single nucleotide resolution tiling array revealed long non-coding transcripts covering the entire FLC locus. The most abundant of these are capped and polyadenylated, initiate over a 100 nucleotide window just downstream of the sense polyA site, are differentially spliced and terminate either within the sense gene or its promoter. Their levels correlate with FLC sense transcripts in all mutants and conditions tested except cold treatment. The antisense transcripts were strongly but transiently cold-induced, much earlier than other vernalization markers, and this coincided with reduction in sense FLC transcription but not sense FLC mRNA levels. Addition of the FLC antisense 5'/sense 3' region to a GFP transgene was sufficient to confer cold-induced silencing of thet fusion; however this silencing was not epigenetically manteined. These processes were all independent of the function of the Polycomb proteins required for maintenance of FLC silencing. Our data suggest that FLC antisense transcripts induce transient FLC transcriptional silencing, possibly through promoter interference, with the epigenetic silencing requiring subsequent recruitment of Polycomb machinery.

2009-12-31 | GSE16977 | GEO

Whole genome nucleosome positioning by MNase-Seq on the mouse tumor line, RMA

Project description:We have employed MNase-Seq technology to determine the nucleosome positioning across the Ly49-expressing RMA cell line. This information was compared to the default nucleosome landscape of these cells as predicted by NuPop computations to identify transcription factor binding site regions that significantly deviate from our predictions, potentially indicating an interfering role for nucleosome binding at these sites. We report that expressed Ly49 genes significantly deviate in their nucleosome coverage at AML-1a sites when compared to other, non-expressed Ly49 genes within the same sample. This information has implications for our understanding of NK cell biology, and also presents the Ly49 family as a convenient model system for discovering how various genetic and epigenetic elements impact expression state, since Ly49 genes are stochastically expressed within a given population, but have similar transcription factor requirements. It is our hope that other work on the epigenetic control of gene expression can benefit from this model system.

2016-04-28 | GSE71863 | GEO

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