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… Expand
View on Nature
generegulation.org
235 Citations
Highly Influential Citations
18
Background Citations
64
Methods Citations
30
Results Citations
7

235 Citations

Citation Type

Citation Type

Nucleosome positioning changes during human embryonic stem cell differentiation
TLDR
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. Expand
Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping
TLDR
An accurate method for defining the nucleosome landscape is established and it is shown that nucleosomes occupy DNA targets for a subset of DNA-binding proteins, including CCCTC-binding factor (CTCF) and pluripotency factors. Expand
Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming
TLDR
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. Expand
HMGN1 Modulates Nucleosome Occupancy and DNase I Hypersensitivity at the CpG Island Promoters of Embryonic Stem Cells
TLDR
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. Expand
Nucleosome Organization in Human Embryonic Stem Cells
TLDR
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. Expand
Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development.
TLDR
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. Expand
Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells
TLDR
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. Expand
Nucleosome repositioning during differentiation of a human myeloid leukemia cell line
TLDR
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. Expand
Genome-wide Nucleosome Occupancy and Organization Modulates the Plasticity of Gene Transcriptional Status in Maize.
Nucleosomes are fundamental units of chromatin that play critical roles in gene regulation by modulating DNA accessibility. However, their roles in regulating tissue-specific gene transcription are… Expand
Defining the chromatin structure of the human genome using size-selected nucleosome mapping
TLDR
The work in this thesis examines genome-wide and local changes in the patterns of nucleosome positioning throughout the human genome to provide insight into the role of chromatin structure in the regulation of human neural cell differentiation. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 62 REFERENCES
Dynamic Regulation of Nucleosome Positioning in the Human Genome
TLDR
It is found that nucleosome phasing relative to the transcription start sites is directly correlated to RNA polymerase II (Pol II) binding and the first nucleosomes downstream of a start site exhibits differential positioning in active and silent genes. Expand
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
TLDR
The application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells is reported and it is shown that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. Expand
Genome-Scale Identification of Nucleosome Positions in S. cerevisiae
TLDR
A tiled microarray approach was developed to identify at high resolution the translational positions of 2278 nucleosomes over 482 kilobases of Saccharomyces cerevisiae DNA, including almost all of chromosome III and 223 additional regulatory regions, strongly suggesting that nucleosome positioning is a global determinant of transcription factor access. Expand
A novel mechanism of epigenetic regulation: nucleosome-space occupancy.
TLDR
It is proposed that nucleosome-space occupancy as a novel mechanism of epigenetic gene regulation, creating a vital environment for transcriptional activation, is proposed. Expand
Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1.
TLDR
It is shown that the catalytic subunit BRG1 of BAF complexes localizes to these distal sites during differentiation and generates a longer nucleosome linker region surrounding the GATA1 sites by shifting the flanking nucleosomes away. Expand
Determinants of nucleosome organization in primary human cells
TLDR
This work uses deep sequencing to map nucleosome positions in three primary human cell types and in vitro and unveils an interplay of sequence-based nucleosomal preferences and non-nucleosomal factors in determining nucleosomes organization within mammalian cells. Expand
CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells
TLDR
Five distinct chromatin domains are uncovered that suggest potential new models of CTCF function in chromatin organization and transcriptional control, and demarcate chromatin-nuclear membrane attachments and influence proper gene expression through extensive cross-talk between promoters and regulatory elements. Expand
Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells.
TLDR
Findings identify rate-limiting targets for transcription regulation during cell differentiation by mapping the density and orientation of transcriptionally engaged RNA polymerases in mouse embryonic stem cells and mouse embryonic fibroblasts. Expand
Histone H1 Depletion in Mammals Alters Global Chromatin Structure but Causes Specific Changes in Gene Regulation
TLDR
Results indicate that linker histones can participate in epigenetic regulation of gene expression by contributing to the maintenance or establishment of specific DNA methylation patterns. Expand
Stable and dynamic nucleosome states during a meiotic developmental process.
TLDR
These findings suggest that, during meiosis, the basic features of genomic chromatin organization are essentially a fixed property of chromosomes, but tweaked in a restricted and program-specific manner. Expand
...
1
2
3
4
5
...