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The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
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The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
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Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
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A Method to Study de novo Formation of Chromatin Domains
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Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation.

Sharmistha Kundu1, Fei Ji1, Hongjae Sunwoo1

  • 1Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

Molecular Cell
|February 4, 2017
PubMed
Summary

Polycomb group (PcG) proteins form small, discrete chromatin domains to stably silence master regulatory genes. These Polycomb repressive complex 1 (PRC1) domains are crucial for epigenetic gene silencing during development.

Keywords:
5CPRC1PolycombSTORMcell fatechromatincompactiondifferentiationhigher-order structure

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Area of Science:

  • Epigenetics
  • Developmental Biology
  • Chromatin Biology

Background:

  • Master regulatory genes require stable silencing by Polycomb group (PcG) proteins for proper differentiation and development.
  • While PcG proteins' histone modification roles are known, their impact on chromatin structure is less understood.

Purpose of the Study:

  • To investigate the higher-order chromatin organization of PcG target genes in embryonic stem cells (ESCs) and neural progenitors.
  • To understand the role of Polycomb repressive complex 1 (PRC1) in forming these structures and their dynamics during differentiation.

Main Methods:

  • 5C (Carbon Copy Chromosome Conformation Capture) technology to analyze genome-wide interactions.
  • Super-resolution microscopy to visualize chromatin organization at high resolution.
  • Analysis of Polycomb repressive complex 1 (PRC1) binding and its components, including Polyhomeotic.

Main Results:

  • Repressed PcG target genes form discrete, compact domains (20-140 Kb) of tight interaction, corresponding to PRC1 binding sites.
  • These PRC1-bound domains change dynamically during differentiation as PRC1 binding is altered.
  • Domain formation is dependent on the Polyhomeotic component of PRC1 and occurs independently of PRC1-catalyzed ubiquitylation.

Conclusions:

  • PRC1 forms distinct chromatin domains that differ in size and boundary characteristics from topologically associating domains.
  • These PRC1 domains are critical for establishing and maintaining epigenetic silencing of PcG targets.
  • PRC1-mediated higher-order chromatin structure plays a key role in transmitting epigenetic silencing during development.