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ABSTRACT: Neurospora crassa MNase (Micrococcal nuclease) seq

PROVIDER: PRJNA386169 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5526334_1.fastq.gz	Fastqsanger.gz
	SRR5526334_2.fastq.gz	Fastqsanger.gz
	SRR5526335_1.fastq.gz	Fastqsanger.gz
	SRR5526335_2.fastq.gz	Fastqsanger.gz
	SRR5526336_1.fastq.gz	Fastqsanger.gz

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Neurospora crassa strain:87-3

Project description:Neurospora crassa MNase (Micrococcal nuclease) seq

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Project description:We examine the effect of this interaction on gene expression and chromatin structure using precision run-on sequencing (PRO-seq) and micrococcal nuclease sequencing (MNase-seq) after RNAi-mediated knockdown in cultured S2 cells. We examine the effect of the interaction between BEAF and polybromo on gene expression and chromatin structure using precision run-on sequencing (PRO-seq) and micrococcal nuclease sequencing (MNase-seq) after RNAi-mediated knockdown in cultured S2 cells.

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Genomic analysis of N. crassa histone H1

Project description:Histone H1 variants, known as linker histones, are essential chromatin components in higher eukaryotes, yet compared to the core histones relatively little is known about their in vivo functions. The filamentous fungus Neurospora crassa encodes a single H1 protein that is not essential for viability. To investigate the role of N. crassa H1, we constructed a functional FLAG-tagged H1 fusion protein and performed genomic and molecular analyses. Cell fractionation experiments showed that H1-FLAG is a chromatin binding protein. Chromatin-immunoprecipitation combined with sequencing (ChIP-seq) revealed that H1-3XFLAG is globally enriched throughout the genome with a subtle preference for promoters of expressed genes. In mammals, the stochiometery of H1 impacts nucleosome repeat length. To determine if H1 impacts nucleosome occupancy or nucleosome positioning in N. crassa, we performed micrococcal nuclease digestion in wildtype and the ∆hH1 strain followed by sequencing (MNase-Seq). Deletion of hH1 did not significantly impact nucleosome positioning or nucleosome occupancy. Analysis of DNA methylation using methylC-sequencing (mC-Seq) revealed a modest but global increase in DNA methylation in the ∆hH1 mutant. Together, these data suggest that H1 acts as a non-specific chromatin binding protein that can limit accessibility of the DNA methylation machinery in N. crassa.

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Chromatin landscape of Leishmania major

Project description:We sought to identify nuclease-hypersensitive sites and to quantify nucleosome positions in an effort to identify cis-regulatory elements in the protozoan parasite Leishmania major. Using micrococcal nuclease digestion of chromatin (MNAse-seq), we report that few nuclease hypersensitive sites are present within the presumed regions of RNA polymerase II-mediated transcription initiation, and that similar numbers of nuclease hypersensitive sites were found in control datasets. However, utilizing an independent approach (FAIRE), we observe that a heterogeneous population of nuclease hypersensitive sites are present in and around these regions, and that nucleosomes within these regions are susceptible to MNAse overdigestion.

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Nucleosome positioning in the IMR90 cell line

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Project description:The nucleosome plays a central role in genome regulation. Traditional methods for mapping nucleosomes depend on the resistance of the nucleosome core to micrococcal nuclease (MNase). However, the lengths of the protected DNA fragments are heterogeneous, limiting the accuracy of nucleosome position information. To resolve this problem, we removed residual linker DNA by simultaneous digestion of yeast chromatin with MNase and exonuclease III (ExoIII). Paired-end sequencing of mono-nucleosomes revealed not only core particles (145-147 bp), but also intermediate particles in which ~8 bp project from one side (154 bp) or both sides (161 bp) of the nucleosome core. We term these particles "pseudo-chromatosomes" because they are present in yeast lacking linker histone. They are also observed after MNase-ExoIII digestion of chromatin reconstituted using recombinant core histones. We propose that the pseudo-chromatosome provides a DNA framework to facilitate H1 binding. Comparison of budding yeast nucleosome sequences obtained using micrococcal nuclease (MNase-seq) and MNase + exonuclease III (ExoIII) (MNase-ExoIII-seq): wild type cells and hho1-null cells. Nucleosome sequences from native chromatin and H1-depleted chromatin from mouse liver. Nucleosome sequences from a plasmid reconstituted into nucleosomes using recombinant yeast histones or native chicken erythrocyte histones.

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Project description:In this study we developed MPE-seq, a method for the genome-wide characterization of chromatin that involves the digestion of nuclei with methidiumpropyl-EDTA-Fe(II) [MPE-Fe(II)] followed by massively parallel sequencing. Like micrococcal nuclease (MNase), MPE-Fe(II) preferentially cleaves the linker DNA between nucleosomes. We also performed MNase-seq as a comparison. We further performed ChIP-seq using chromatin samples obtained by MPE-Fe(II) or MNase digestion of nuclei.

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Project description:We produced a map of nucleosome positions in IMR90 by sequencing the ends of MNase-digested chromatin fragments. IMR90 cells were grown in culture, about 1E6 cells were isolated and digested using micrococcal nuclease (MNase). Mononucleosomes were gel-selected and fragment ends were sequenced using the Illumina GAIIx sequencing platform.

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