Lecture 20 Chromatin

Cell and Chromatin Basics

  • Cell: Basic unit of life.
  • Chromosome: Structure that houses DNA.
  • Histones: Major DNA-binding proteins involved in chromatin formation.
  • DNA: Genetic material, packaged in a highly organized structure.
  • Chromatin: Complex of DNA and proteins in the eukaryotic nucleus, facilitating compaction and gene regulation.

Types of Chromatin

  • Euchromatin:
    • Less condensed form of chromatin, generally transcriptionally active.
    • Features include:
    • CpG hypomethylation (lower methylation levels).
    • Early replication during the cell cycle.
    • Gene-rich areas.
    • Stains less intensely with DNA dyes.
  • Heterochromatin:
    • Highly condensed form of chromatin, usually transcriptionally inactive.
    • Types include:
    • Constitutive: Present in all cells, consists of repetitive DNA (satellite DNA, telomeric, centromeric).
    • Facultative: Can be converted to euchromatin; regulated during differentiation.

Chromatin Structure

  • Histones Composition:
    • 60% protein, 30% DNA, 10% RNA with a bulk being histones.
    • Histones are alkaline and facilitate packaging of negatively charged DNA.
  • Nucleosomes:
    • Fundamental unit of chromatin, consists of DNA wrapped around a core of histone proteins (H2A, H2B, H3, H4).
    • Each nucleosome covers about 200 bp of DNA.
    • Linker DNA connects nucleosomes, bound by histone H1.

Levels of Chromatin Organization

  • 10 nm Fiber: Represented as 'beads on a string', composed of nucleosomes.
  • 30 nm Fiber: Organized structure that further compacts DNA during interphase and metaphase.
  • DNA Accessibility: Nucleosomes restrict access and determine the sites for transcription, affecting gene expression due to their phasing and positioning in relation to regulatory sequences.

Nucleosome Positioning

  • Intrinsic Factors: Favor certain positions based on DNA sequence (e.g., A-T rich regions are more flexible).
  • Extrinsic Factors: Include binding proteins and regulatory elements that exclude nucleosomes from specific regions, influencing transcriptional activity.
  • Consequences: Proper positioning affects access to DNA and gene regulation, determining whether sequences are exposed or require remodeling for transcription.

Chromatin Assembly and Dynamics

  • Replication-Coupled Assembly:
    • Involves the transfer of parental histones and de novo assembly facilitated by chromatin assembly factors (CAF1 and ASF1).
    • This process ensures rapid and proper repackaging of replicated DNA into chromatin.

DNase I Hypersensitivity

  • Definition: Sites more susceptible to DNase I cleavage are indicative of accessible chromatin (active transcription regions).
  • Significance: DHS sites are prominent near regulatory elements like enhancers and promoters of active genes.

Insulators and Gene Regulation

  • Insulators: DNA elements that prevent activation by enhancers or repression by heterochromatin; critical for maintaining specific gene expression patterns.
  • Activities: Can exhibit barrier or enhancer-blocking capabilities, ensuring discrete regulation between adjacent genes.

Special Chromatin Structures and Regulation

  • Heat Shock Genes: Exhibit special structures (e.g., scs regions) that become accessible during stress responses, indicating organization and regulation of chromatin by insulators and protein factors.
  • Loop Domains: Interactions among insulators facilitate the isolation of gene clusters for regulated expression, crucial during cellular stress events.