Genomes are complex structures containing genes, regulatory sequences, and non-coding DNA. These components work together to control gene expression and cellular function. Understanding genome organization is crucial for grasping how genetic information is stored and utilized.

Chromatin structure and repetitive elements play key roles in genome function. Chromatin packaging affects gene accessibility, while repetitive DNA sequences contribute to genome size and evolution. These factors influence gene expression and genetic variation within populations.

Genome Components and Organization

Components of a genome

• Genes encode functional products (proteins or RNA) and consist of:
  • Exons which are coding regions that directly contribute to the final gene product
  • Introns which are non-coding intervening sequences that are spliced out during RNA processing
• Regulatory sequences control gene expression by modulating transcription rates
  • Promoters initiate transcription by providing binding sites for RNA polymerase and transcription factors (TATA box)
  • Enhancers increase transcription rate and can be located upstream or downstream of the gene (locus control regions)
  • Silencers decrease transcription rate by binding repressive transcription factors (neuron-restrictive silencer element)
  • Insulators block interactions between enhancers and promoters, preventing inappropriate gene activation (CTCF binding sites)
• Non-coding DNA does not encode proteins but plays important roles in genome structure and function
  • Intergenic regions are stretches of DNA located between genes (gene deserts)
  • Pseudogenes are non-functional gene remnants that have lost their coding ability due to mutations (olfactory receptor pseudogenes)
  • Telomeres are repetitive sequences at chromosome ends that protect them from degradation and fusion (TTAGGG repeats)
  • Centromeres are regions where spindle fibers attach during cell division to ensure proper chromosome segregation (alpha satellite DNA)

Prokaryotic vs eukaryotic genomes

• Prokaryotic genomes have a circular chromosome, lack a membrane-bound nucleus, and have genes arranged in operons
  • Operons allow polycistronic transcription where multiple genes are transcribed as a single mRNA (lac operon)
  • Prokaryotic genomes have fewer regulatory sequences and minimal intergenic regions
• Eukaryotic genomes have linear chromosomes, a membrane-bound nucleus, and genes arranged individually
  • Monocistronic transcription produces one mRNA per gene
  • Eukaryotic genomes have more complex regulatory sequences, larger intergenic regions, and the presence of introns and exons

Chromatin Structure and Repetitive Elements

Chromatin structure in gene regulation

• Chromatin is the complex of DNA and associated proteins that packages DNA into a compact form
• Nucleosomes are the basic unit of chromatin, consisting of DNA wrapped around histone proteins (H2A, H2B, H3, H4)
• Chromatin states influence gene expression
  • Euchromatin is less condensed and transcriptionally active (open chromatin)
  • Heterochromatin is highly condensed and transcriptionally inactive (closed chromatin)
• Histone modifications alter chromatin structure and gene expression
  • Acetylation of lysine residues is associated with active transcription (H3K9ac)
  • Deacetylation of lysine residues is associated with repressed transcription
  • Methylation can activate or repress transcription depending on the residue (H3K4me3 activates, H3K9me3 represses)
• DNA methylation involves the addition of methyl groups to cytosine residues and is associated with transcriptional repression (CpG islands)

Significance of repetitive DNA

• Repetitive DNA sequences are repeated multiple times throughout the genome
  • Tandem repeats are repeated sequences adjacent to each other
    1. Microsatellites are short tandem repeats of 2-10 base pairs (CA repeats)
    2. Minisatellites are longer tandem repeats of 10-100 base pairs (variable number tandem repeats)
  • Interspersed repeats are repeated sequences scattered throughout the genome
    1. SINEs (Short Interspersed Nuclear Elements) are 100-300 base pairs long (Alu elements)
    2. LINEs (Long Interspersed Nuclear Elements) are 1,000-7,000 base pairs long (LINE-1 elements)
• Transposable elements are mobile genetic elements that can move within the genome
  • DNA transposons move via a "cut and paste" mechanism (Ac/Ds elements in maize)
  • Retrotransposons move via a "copy and paste" mechanism using an RNA intermediate
    1. LTR (Long Terminal Repeat) retrotransposons have long terminal repeats at their ends (endogenous retroviruses)
    2. Non-LTR retrotransposons lack LTRs (LINE-1, SINE elements)
• Repetitive elements play significant roles in genome evolution and function
  • They contribute to genome size and evolution by increasing genetic material
  • They can influence gene expression and regulation by providing regulatory sequences or altering chromatin structure
  • Insertional mutagenesis occurs when a transposable element insertion disrupts gene function (hemophilia A caused by LINE-1 insertion)
  • Repetitive elements are a source of genetic variation and diversity within populations