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Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize [MNase-seq]

ABSTRACT: Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize [MNase-seq]

PROVIDER: PRJNA938032 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23597545_1.fastq.gz	Fastqsanger.gz
	SRR23597545_2.fastq.gz	Fastqsanger.gz
	SRR23597546_1.fastq.gz	Fastqsanger.gz
	SRR23597546_2.fastq.gz	Fastqsanger.gz
	SRR23597547_1.fastq.gz	Fastqsanger.gz

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Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize [MNase-seq]

Project description:Distinct nucleosome architectures decode key regulatory information related to various cellular processes. However, how fragile (Fra-Nus) and resistant (Res-Nus) nucleosomes, with sensitivity and resistance to MNase cleavage, respectively, are reprogrammed and their potential biological implications under cold treatment is completely uncharacterized in plants. To this end, we conducted MNase-seq with light, medium and heavy MNase digestion in combination with multi-omics data (RNA-seq, ChIP-seq, MH-seq and resequencing data) between COLD and CK.

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Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize [RNA-seq]

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Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize [ChIP-seq]

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Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize [MH-seq]

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MNase digestion-sensitive nucleosomes in Saccharomyces cerevisiae

Project description:The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity – nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed fragile nucleosomes throughout the yeast genome, nearly one thousand of which are at previously determined “nucleosome free” loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization. Comparing nucleosome occupancy under different MNase digestion levels and growth conditions.

2011-01-24 | E-GEOD-26412 | biostudies-arrayexpress

MNase-sensitive complexes in yeast: nucleosomes and non-histone barriers

Project description:Micrococcal nuclease (MNase) is commonly used to map nucleosomes genome-wide, but nucleosome maps are affected by the degree of digestion. It has been proposed that many yeast promoters are not nucleosome-free but occupied by easily digested, unstable, “fragile” nucleosomes. We analyzed the histone content of all MNase-sensitive complexes by MNase-ChIP-seq and Sonication-ChIP-seq. We find that yeast promoters are predominantly bound by non-histone protein complexes, with little evidence for fragile nucleosomes. We do detect MNase-sensitive nucleosomes elsewhere in the genome, including transcription termination sites. However, they have high A/T-content, suggesting that MNase sensitivity does not indicate instability, but the preference of MNase for A/T-rich DNA, such that A/T-rich nucleosomes are digested faster than G/C-rich nucleosomes. We confirm our observations by analyzing ChIP-exo, chemical mapping and ATAC-seq data from other laboratories. Thus, histone ChIP-seq experiments are essential to distinguish nucleosomes from other DNA-binding proteins that protect against MNase.

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Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize

Project description:Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize

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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.

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Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize [MH-seq]

Project description:Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize [MH-seq]

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