Chromatin and DNA Packaging Notes

Chromatin and DNA Packaging

Chromosome Structure

  • Sister Chromatids: Two identical copies of a single chromosome.
  • Centromere: The region where sister chromatids are most closely attached.
  • Chromosome (before DNA replication): A single DNA molecule.
  • Chromosome (after DNA replication): Two sister chromatids attached at the centromere.

DNA Packaging and Scale

  • Humans have 22 pairs of autosomes and 1 pair of sex chromosomes, totaling 23 chromosome pairs.
  • This equates to 46 chromosomes.
  • The human genome contains approximately 6 billion base pairs (6×1096 \times 10^9).
  • The distance between base pairs is 0.34×10−90.34 \times 10^{-9} meters.
  • The total length of DNA in a cell is approximately 2 meters (6.5 feet), calculated as: (6×109 base pairs)×(0.34×10−9 m/base pair)≈2 meters(6 \times 10^9 \text{ base pairs}) \times (0.34 \times 10^{-9} \text{ m/base pair}) \approx 2 \text{ meters}.
  • Scale of organization: Cell (10 nm) to 2 meters of DNA.

Chromatin

  • Chromatin is the complex of DNA and protein (histones).
  • Chromatin undergoes condensation to form metaphase chromosomes.
Types of Chromatin:
  • Euchromatin: Lightly packed, gene-rich, and actively transcribed.
  • Heterochromatin: Tightly packed, genetically inactive sequences.
    • Constitutive heterochromatin: Very gene-poor regions like centromeres and telomeres.
    • Facultative heterochromatin: Regions subject to gene silencing, such as Barr bodies.

Models of DNA and Protein Association

Folded Fiber Model (Dupraw, 1965)
  • Based on whole mounts of human white blood cells.
  • Proposed each chromatid consists of a single fiber due to the lack of free fiber ends.
  • Type A Fiber: 1-10 nm (ratio of ~6:1).
  • Type B Fiber: 20-25 nm (ratio of ~10:1).
  • Extensive folding of Type B fibers forms a chromatid.
  • Replication proceeds from each end towards the centromere.
Nucleosome Model (Kornberg, 1974; Oudet, 1975)
  • Most commonly accepted model for DNA packaging.
  • Nucleosome: The simplest packaging structure of eukaryotic chromatin.
  • Localized areas of transcription are a better fit for protein biosynthesis.
Classes of Histones:
  • Core Histones: H2A, H2B, H3, and H4.
    • Highly conserved during evolution.
    • Each consists of approximately 120 amino acids.
    • Form the core particle.
    • Very basic in charge, with approximately 25% Lysine and Arginine.
  • Linker Histone: H1.
    • Tissue-specific expression and not highly conserved.
    • Consists of approximately 200 amino acids.
    • Loosely associated with the core particle.

Nucleosome Formation

  • 200 base pairs (bp) of DNA are involved in nucleosome formation.
  • 146 bp wrap around the histone core.
  • 54 bp link to the next nucleosome (Linker DNA).
  • The nucleosome forms a 10 nm fiber, representing the primary packaging of chromatin.
  • This reduces the DNA length by approximately 7 times.
  • The arrangement is described as "beads on a string".

Super Coiling and Solenoid Formation

  • Histone H1 is responsible for packaging DNA into a solenoid structure.
  • Solenoid: Helical coiling of 10 nm fibers, consisting of 6 nucleosomes.
  • Supercoiling reduces the length of DNA by approximately 7 times, leading to a compaction of 40X.
Histone H1 Function
  • Binds two distinct regions of DNA:
    1. Linker DNA.
    2. A portion of the 146 bp core.
Alternate Model: Zig Zag Model
  • The DNA backbone may not be flexible enough to bend between nucleosomes.
  • Straight linker DNA connects opposite nucleosomes.
  • Experimental results suggest that both solenoid and zig-zag topologies may be simultaneously present in chromatin fibers.

Higher Order Coiling

  • Forms a 300 nm fiber called "Chromatin loops".
  • Built around a scaffold of Topoisomerase II.
  • Represents the final condensation level of euchromatin.
  • Metaphase chromosome: DNA diameter is approximately 700 nm.
  • The spiral scaffold is composed of Topoisomerase II and about 15 non-histone proteins.
  • Represents the compaction level of heterochromatin.

Chromatin Formation and the Cell Cycle

  • Chromatin structure transitions through various stages:
    • 2 nm (DNA) -> 10 nm fiber
    • 30 nm fiber
    • 300 nm fiber
    • 700 nm chromatin
    • Chromosome

Karyotype

  • A picture of metaphase chromosomes in the nucleus of eukaryotic cells.
  • Uses classic (Geimsa stain) or spectral staining (fluorescent probes).
  • Allows for analysis of:
    • Chromosome size
    • Centromere position
    • Heterochromatin vs. euchromatin

Summary of DNA Packaging

  • Large DNA molecules must be highly condensed to fit within the nucleus of a cell.
  • Condensation occurs in stages:
    • Nucleosomes
    • Solenoids
    • Chromatin Loops
    • Condensed Chromatin
    • Chromatin folded around a protein scaffold
  • Chromosome condensation is intimately associated with the cell cycle.

Genome Complexity and Gene Structure

  • Considered the next topic.