Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA254343 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1506590_1.fastq.gz | Fastqsanger.gz | |||
| SRR1506590_2.fastq.gz | Fastqsanger.gz | |||
| SRR1506591_1.fastq.gz | Fastqsanger.gz | |||
| SRR1506591_2.fastq.gz | Fastqsanger.gz | |||
| SRR1506592.fastq.gz | Fastqsanger.gz |
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Project description:The nucleosome is a fundamental unit of chromatin architecture, but it has been under-evaluated during the analysis of histone modification using ChIP-Seq. Thus, we developed a novel approach for defining histone modification at single nucleosome resolution by synergistic analyses of histone modification data from ChIP-Seq and high-resolution nucleosome mapping data from native MNase-Seq using a PCR-free strategy. With this approach, we have generated histone modification data at the single nucleosome resolution in human embryonic stem cells, normal hepatocytes, and liver cancer cells of both genders, and performed quantitative analysis of epigenetic regulation in stem cell differentiation into hepatocytes and neoplastic transformation of liver cancer.
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Project description:We determined genome-wide nucleosome occupancy in mouse embryonic stem cells and their neural progenitor and embryonic fibroblast counterparts to assess features associated with nucleosome positioning during lineage commitment. Cell type and protein specific binding preferences of transcription factors to sites with either low (e.g. Myc, Klf4, Zfx) or high (e.g. Nanog, Oct4 and Sox2) nucleosome occupancy as well as complex patterns for CTCF were identified. Nucleosome depleted regions around transcription start and termination sites were broad and more pronounced for active genes, with distinct patterns for promoters classified according to their CpG-content or histone methylation marks. Throughout the genome nucleosome occupancy was dependent on the presence of certain histone methylation or acetylation modifications. In addition, the average nucleosome-repeat length increased during differentiation by 5-7 base pairs, with local variations for specific genomic regions. Our results reveal regulatory mechanisms of cell differentiation acting through nucleosome repositioning.
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Project description:We determined genome-wide nucleosome occupancy in mouse embryonic stem cells and their neural progenitor and embryonic fibroblast counterparts to assess features associated with nucleosome positioning during lineage commitment. Cell type and protein specific binding preferences of transcription factors to sites with either low (e.g. Myc, Klf4, Zfx) or high (e.g. Nanog, Oct4 and Sox2) nucleosome occupancy as well as complex patterns for CTCF were identified. Nucleosome depleted regions around transcription start and termination sites were broad and more pronounced for active genes, with distinct patterns for promoters classified according to their CpG-content or histone methylation marks. Throughout the genome nucleosome occupancy was dependent on the presence of certain histone methylation or acetylation modifications. In addition, the average nucleosome-repeat length increased during differentiation by 5-7 base pairs, with local variations for specific genomic regions. Our results reveal regulatory mechanisms of cell differentiation acting through nucleosome repositioning.
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