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In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
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Chromatin Immunoprecipitation from Human Embryonic Stem Cells
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Nucleosome positioning changes during human embryonic stem cell differentiation.

Wenjuan Zhang1, Yaping Li1, Michael Kulik1

  • 1a Department of Biochemistry and Molecular Biology , Institute of Bioinformatics, University of Georgia , Athens , GA , USA.

Epigenetics
|April 19, 2016
PubMed
Summary
This summary is machine-generated.

Human embryonic stem cells (hESCs) show distinct nucleosome positioning linked to gene expression. Differentiation to smooth muscle cells (SMCs) reveals a shift in positioning towards GC-rich regions.

Keywords:
G+C contentMNase-seqhESC differentiationnucleosome occupancynucleosome positioningsequence mutationtranscription

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Area of Science:

  • Genomics
  • Epigenetics
  • Cell Biology

Background:

  • Nucleosomes are fundamental chromatin units influencing gene regulation.
  • Nucleosome positioning (NP) is critical for transcriptional control and cellular functions.
  • Understanding NP dynamics during cell differentiation is key to deciphering developmental processes.

Purpose of the Study:

  • To investigate dynamic changes in nucleosome positioning during human embryonic stem cell (hESC) differentiation into mesoderm and smooth muscle cells (SMCs).
  • To correlate nucleosome occupancy with gene expression and sequence composition across differentiation stages.
  • To identify genome-wide alterations in nucleosome positioning associated with cellular transitions.

Main Methods:

  • Micrococcal nuclease digestion followed by sequencing (MNase-seq) was employed to map nucleosome occupancy.
  • Comparative analysis of nucleosome positioning in hESCs, nascent mesoderm, and SMCs.
  • Correlation analysis between nucleosome occupancy, transcript abundance, and genomic sequence content (G+C content, mutation rates).

Main Results:

  • hESCs exhibit stronger correlations between nucleosome occupancy at genic regions and transcript abundance compared to differentiated cells.
  • Gene silencing during hESC differentiation is associated with significant promoter nucleosome occupancy changes, unlike gene activation.
  • A genome-wide shift in nucleosome positioning towards G+C-rich regions was observed during hESC to SMC differentiation.
  • Regions with higher nucleosome occupancy showed increased G↔C changes and decreased A↔T changes.
  • The hESC genome showed no evidence of rearrangement and a mutation rate comparable to normal human genomes.

Conclusions:

  • Nucleosome positioning in hESCs is closely tied to gene expression and less influenced by sequence composition than in differentiated cells.
  • Differentiation involves specific nucleosome remodeling at promoters of silenced genes.
  • A novel association between nucleosome occupancy and G+C content emerges during hESC differentiation.
  • The hESC genome is stable, with nucleosome positioning dynamics offering insights into chromatin regulation.