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The role of nucleosome positioning in the evolution of gene regulation

ABSTRACT: The role of nucleosome positioning in the evolution of gene regulation

PROVIDER: PRJNA126767 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR059724.fastq.gz	Fastqsanger.gz
	SRR059725.fastq.gz	Fastqsanger.gz
	SRR059726.fastq.gz	Fastqsanger.gz
	SRR059727.fastq.gz	Fastqsanger.gz
	SRR059728.fastq.gz	Fastqsanger.gz

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Dynamic regulation of nucleosome positioning in the human genome

Project description:The positioning of nucleosomes with respect to DNA plays an important role in regulating transcription. However, nucleosome mapping has been performed for only limited genomic regions in humans. We have generated genome-wide maps of nucleosome positions in both resting and activated human CD4+ T cells by direct sequencing of nucleosome ends using the Solexa high-throughput sequencing technique. We find that nucleosome phasing relative to the transcription start sites (TSSs) is directly correlated to RNA polymerase II binding. Furthermore, the first nucleosome downstream of TSSs exhibits differential positioning in active and silent genes. TCR signaling induces extensive nucleosome reorganization in promoters and enhancers to allow transcriptional activation or repression. Our results suggest that H2A.Z-containing and modified nucleosomes are preferentially lost from the -1 nucleosome position. Our data provide a comprehensive view of the nucleosome landscape and its dynamic regulation in the human genome. This microarray dataset is the gene expression data from resting and activated CD4+ T cells. We used this data to look at nucleosome positioning, Pol II and a few chromatin modifications at genes that are silent and activated in both resting and activated T cells as well as genes that are induced or repressed with T cell activation. Keywords: nucleosome mapping, expression data complementary to Solexa ChIP-Seq data

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Comparison of nucleosome positioning among two yeast species and their hybrid for wild-type and deletion mutant strains

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The role of nucleosome positioning in the evolution of gene regulation

Project description:This SuperSeries is composed of the following subset Series: GSE22191: Absolute expression level of Debaryomyces hansenii genes GSE22192: Absolute expression level of Yarrowia lipolytica genes GSE22193: Absolute expression level of Saccharomyces paradoxus genes GSE22194: Absolute expression level of Candida glabrata genes GSE22197: Absolute expression level of Candida albicans genes GSE22198: Absolute expression level of Kluyveromyces lactis genes GSE22199: Absolute expression level of Kluyveromyces waltii genes GSE22200: Absolute expression level of Saccharomyces castellii genes GSE22201: Absolute expression level of Saccharomyces mikatae genes GSE22202: Absolute expression level of Saccharomyces kluyveryii genes GSE22204: Absolute expression level of Saccharomyces cerevisiae genes GSE22205: Absolute expression level of Saccharomyces bayanus genes GSE22211: Genome-wide nucleosome position data for 12 yeast species Refer to individual Series

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Noncoding RNA-mediated DNA methylation directs nucleosome positioning

Project description:We explored the mechanism by which RdDM affects nucleosome positioning in Arabidopsis thaliana. We showed that POLV has a direct effect on nucleosomes through the SWI/SNF complex. We found that the AGO4-siRNA complex is involved in nucleosome positioning via IDN2. Moreover, the SWI/SNF complex is not required for DNA methylation in positioned nucleosomes. Instead, we found that DNA methylation is needed for nucleosome positioning in differentially methylated regions. Taken together, we propose a model where the RdDM pathway directs nucleosome positioning through DNA methylation to establish transcriptional gene silencing.

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Comparison of nucleosome positioning among two yeast species and their hybrid for wild-type and deletion mutant strains

Project description:To study the evolution of nucleosome positioning we mapped nucleosome positioning in two species of yeasts. Identified differences in nucleosome positioning were classified into cis-based changes or trans-bseed changes based on the pattern of nucleosomes in the hybrid. This analysis was performed for wild-type strains as well as for strains deleted of 5 chromatin regulatoirs allolwing us to examine their roles in determining nucleosome positioning. Illumina sequencing of mono-nucleosome fragments isolated by MNase digestion. Samples include pooled DNA fragments of S. cerevisiae and S. paradoxus or DNA fragments of the interspecific hybrid. Experiments were performed for WT strains as well as strains deleted of 5 chromatin regulators.

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