DNA Packaging in Bacteria and Eukaryotes

DNA Packaging in Bacteria

• Chromosomal DNA
  • Most bacteria possess circular chromosomal DNA.
  • Typical chromosome length: Few million base pairs.
  • Usually, a single chromosome type exists but may be present in multiple copies.
  • Chromosomes contain thousands of genes with short intergenic regions between them.
• Replication Origin
  • One origin of replication is essential for DNA replication initiation.
  • Repetitive sequences can be found sporadically throughout the chromosome.

DNA Packaging in Eukaryotes

• Chromosomal Structure
  • Eukaryotic chromosomes are linear.
  • Typical chromosome length ranges from tens of millions to hundreds of millions of base pairs.
  • Chromosomes usually occur in sets (e.g., diploid organisms have two sets).
  • Typically, several hundred to thousands of different genes are distributed throughout.
• Replication and Features
  • Origins of replication are present every ~100,000 base pairs.
  • Each chromosome has a centromere for kinetochore protein recognition.
  • Telomeres at each end contain specialized sequences.
  • Common repetitive sequences near centromeres/telomeres and interspersed across chromosomes.

DNA Sequence Composition in the Human Genome

• Classifications
  • Unique sequences: Code for proteins, enhancers, etc.
  • Repetitive DNA: Non-coding regions, regions of genes not found within coding sequences (exons).
  • Introns constitute an additional category.
  • Graph Data: Unique sequences constitute approximately 24%, while repetitive DNA includes a substantial 59%.

Transposable Elements (TEs)

• Types of TEs
  • Transposons (TES): Move through simple transposition or retrotransposition processes.
  • Simple Transposition: Directly moves DNA segments.
  • Retrotransposition: Involves an RNA intermediate and reverse transcriptase.
• Consequences of Transposition
  • Can lead to mutagenesis:
  • Causes chromosome breakage and rearrangements.
  • Induces mutations and may result in gene inactivation or alteration of gene expression.
  • Exon Shuffling: Inserts exons into existing gene sequences through TEs.

Abundance of Transposable Elements Across Species

• Species and TE Genome Percentage:
  • Xenopus laevis: 77%
  • Zea mays: 60%
  • Homo sapiens: 45%
  • Mus musculus: 40%
  • Drosophila melanogaster: 20%
  • Caenorhabditis elegans: 20%
  • Saccharomyces cerevisiae: 12%
  • Escherichia coli: 4%
  • Note: Variation in TE abundance can exist among strains within a species.

Levels of DNA Packaging in Eukaryotes

1. Nucleosome Structure
   • Comprised of histone octamers wrapped around DNA (146-147 bp).
   • Nucleosomes present the DNA as "beads on a string".
2. 30 nm Fiber
   • Further coiling into a thicker structure, also known as the solenoid structure.
3. Radial Looping
   • Loop domains anchored to protein filaments, creating higher-order structures.
4. Metaphase Chromosomes
   • Highly condensed and accessible for individual chromosomal analysis during cell division.

Summary of Chromosome Features

• Basic Structure: Telomeres, Centromeres, Euchromatin, and Heterochromatin.
• Compaction Levels: From 2 nm (DNA helix) to 1400 nm chromosomal structures during metaphase, each stage involves significant structural formations to enable effective gene deployment and protection during cellular processes.