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

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

PROVIDER: PRJNA938027 | ENA |

REPOSITORIES: ENA

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

2025-02-01 | GSE225909 | GEO

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

2025-02-01 | GSE225916 | GEO

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

2025-02-01 | GSE225914 | GEO

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

2025-02-01 | GSE225907 | GEO

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

| PRJNA938025 | ENA

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

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

| PRJNA938032 | ENA

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

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

| PRJNA938033 | ENA

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

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

| PRJNA938021 | ENA

Characterization of distinct types of open chromatin and their impacts on gene transcription in maize [MH-seq]

Project description:Open chromatin plays key roles in regulating gene expression in eukaryotic genomes. However, functional implications of fragile nucleosome overlapping open chromatin are still largely unknown, especially in plants. Here, through simultaneous measurement of MHSs and nucleosomes, we detected two distinct types of open chromatin, one with nucleosome-free (type-I MHSs) and the other with fragile nucleosomes (type-II MHSs) in maize and Arabidopsis. Both types of MHSs can function as cis-regulatory elements and have similar TF binding motifs. Furthermore, fragile nucleosomes with MHSs have unique DNA sequence features with less AT and more GC dinucleotides, whereas other fragile nucleosomes without overlapping MHSs have more AT and less GC dinucleotides. In particular, we observed distinct fragile nucleosome positioning patterns occurred around the summit of type-I and type-II MHSs, phased fragile nucleosome arrays and only two well-phased fragile nucleosomes surrounding the summit of type-I and type-II MHSs, respectively. We finally found that type-II MHS-related genes with BCTSS or SCTSS express more than type-I-related genes with the corresponding CTSS, which is mediated by combined actions of MHSs with TFs, fragile nucleosomes, Pol II and epigenetic marks.

2023-08-27 | GSE157149 | 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

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