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Drosophila melanogaster

ABSTRACT: ACF1 regulates nucleosome spacing in Drosophila euchromatin [ChIP-seq]

PROVIDER: PRJNA338341 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4017020.fastq.gz	Fastqsanger.gz
	SRR4017021.fastq.gz	Fastqsanger.gz
	SRR4017022.fastq.gz	Fastqsanger.gz
	SRR4017019.fastq.gz	Fastqsanger.gz

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Drosophila melanogaster

Project description:ACF1 regulates nucleosome spacing in Drosophila euchromatin [Mnase-seq embryos]

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ACF1 regulates nucleosome spacing in Drosophila euchromatin

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ACF1 regulates nucleosome spacing in Drosophila euchromatin [ChIP-seq]

Project description:The nature of chromatin as regular succession of nucleosomes has gained iconic status. The average nucleosome repeat length (NRL) determined by classical means serves as index for bulk chromatin of a given specimen. However, this value is dominated by regular heterochromatin since nucleosomal arrays are often not regular at individual single copy sequences. To obtain a measure for nucleosome regularity in euchromatin we subjected nucleosome dyad profiles to autocorrelation and spectral density analyses. This revealed variation in nucleosome regularity and NRL at different types of euchromatin and yielded a comprehensive catalog of regular phased nucleosome arrays (PNA). The absence of the nucleosome sliding factor ACF1 correlated with global loss of regularity in euchromatin and increased NRL and compromised phasing at a novel type of PNA. Our approach is generally applicable to characterize hallmarks of euchromatin organization.

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Project description:Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos[ChIP-Seq]

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Active Promoters give rise to false positive 'Phantom Peaks' in ChIP-Seq experiments

Project description:We applied ChIP-seq to map the chromosomal binding sites for two nucleosome remodeling complexes containing the ATPase ISWI, ACF and RSF, in Drosophila embryos. Employing a panel of polyclonal and monoclonal antibodies directed against their signature subunits, ACF1 and RSF1, robust profiles were obtained indicating that both remodelers co-occupied a large set of active promoters. For further validation we repeated the mapping using chromatin of mutant embryos that do not express ACF1 or RSF1. Surprisingly, the ChIP-seq profiles were unchanged, suggesting that they were not due to specific immunoprecipitation. Conservative analysis lists about 3000 chromosomal loci, mostly active promoters that are prone to non-specific enrichment in ChIP and give rise to ‘Phantom Peaks’. These peaks are not obtained with pre-immune serum and are not prominent in input chromatin. Examination of various ACF1 and RSF1 antibodies in Drosophila melanogaster embryos which are wildtype or mutant for the antibody targets.

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