Genome-wide nucleosome positioning during embryonic stem cell development

@article{Teif2012GenomewideNP,
  title={Genome-wide nucleosome positioning during embryonic stem cell development},
  author={Vladimir B. Teif and Yevhen Vainshtein and Ma{\"i}wen Caudron-Herger and Jan-Philipp Mallm and Caroline Marth and Thomas H{\"o}fer and Karsten Rippe},
  journal={Nature Structural \&Molecular Biology},
  year={2012},
  volume={19},
  pages={1185-1192}
}
We determined genome-wide nucleosome occupancies 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 (Myc, Klf4 and Zfx) or high (Nanog, Oct4 and Sox2) nucleosome occupancy as well as complex patterns for CTCF were identified. Nucleosome-depleted regions around… 
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Nucleosome positioning changes during human embryonic stem cell differentiation

The analysis indicates that the hESC genome is not rearranged and has a sequence mutation rate resembling normal human genomes, and sheds light on the relationship between nucleosome occupancy and sequence G+C content.

Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping

Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming

It is concluded that changes in nucleosome occupancy are a hallmark of cell differentiation and reprogramming and likely identify regulatory regions essential for these processes.

HMGN1 Modulates Nucleosome Occupancy and DNase I Hypersensitivity at the CpG Island Promoters of Embryonic Stem Cells

It is shown that HMGN1, a nucleosome-binding protein ubiquitously expressed in vertebrate cells, preferentially binds to CpG island-containing promoters and affects the organization of nucleosomes, DNase I hypersensitivity, and the transcriptional profile of mouse embryonic stem cells and neural progenitors.

Nucleosome Organization in Human Embryonic Stem Cells

Ultra-deep sequencing of nucleosomal DNA in two human embryonic stem cell lines and integrated data with numerous epigenomic maps suggest that nucleosome organization is associated with numerous genomic and epigenomic processes and can be used to elucidate cellular identity.

DNA Sequence-Dependent Properties of Nucleosome Positioning in Regions of Distinct Chromatin States in Mouse Embryonic Stem Cells

By developing an improved deformation-energy-based model, some sequence-dependent properties of the nucleosome arrangements in regions of distinct chromatin states in mouse ESCs are revealed.

Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development

The linkages between DNA methylation, hydroxymethylation, nucleosome repositioning, and binding of the transcription factor CTCF during differentiation of embryonic stem cells are dissected and a quantitative biophysical model of competitive binding with the histone octamer is modeled.

Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells

The dynamics and critical roles of nucleosome positioning and chromatin organization in gene regulation during reprogramming are revealed and it is demonstrated that pre-iPSCs have a more open and phased chromatin architecture than that of MEFs and iPSCs.

Nucleosome repositioning during differentiation of a human myeloid leukemia cell line

Ch chromatin changes during HL-60/S4 differentiation appeared to be more localized to regulatory regions, compared with genome-wide changes among diverse cell types studied elsewhere.

Genome-wide Nucleosome Occupancy and Organization Modulates the Plasticity of Gene Transcriptional Status in Maize.

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