Lecture 3: Genome Organization

Genome organization varies in different organisms

2 genome classes

Packing of the eukaryotic genome

• Problem

  • How to fit 2 meters of DNA into a 10um space

• Solution

  • Double-stranded linear DNA packed into chromatin (DNA + histones)

Genomes composed of chromosomes in cells

Chromatin: composed of chromosome DNA and histones

Nucleosomes

• Core octamer of histones plus one molecule of the linker
  histone.

• 180 bp DNA wound around, left-handed (positive/negative supercoiling??)

left= denature= Negative supercoil

partial digestions of chromosome using DNase reveals nucleosome structure

-isolate chromatin and use DNAase

Histones are small, positively charged proteins

• 2 types of histones

  • highly conserved core histones

  • more variable linker histones

Why are they positively charged???

• Bc DNA molecule are negative

Core histones

• small, positively-charged, basic proteins

• Histones

  • H2A, H2B, H3, H4

• Rich in arginine and lysine

  • bc epigenetic modification, each are highly modified in body, and positively charged

• 146 bp of negatively charged DNA wraps nearly twice around the positively charged octamers

Linker histones

• larger than core histones, positively-charged, basic proteins

• Histones H1, H5, H1’,etc (NO REMEMBER)

• between core octamers

Some cells do not possess histones

• Protamine

  • Sperm DNA compacted with basic proteins

N and C terminal so of histones play critical roles

• Carboxyl (C) terminal end
  • Extended histone-fold domain
  • Histone-histone interactions
  • Histone-DNA interactions
  

• Amino (N) terminal charged “tails”
  • Lysine-rich

  • highly modified
    • Sites of many post-translational modifications

Further packaging of DNA involves loop domains

Insight into loop structure comes from studies of lampbrush chromosomes in amphibian oocytes

Fully condensed: metaphase chromosomes

packing ration of 10,000 fold

The centromere provides the site of attachment for segregation during cell division

• A fully condensed metaphase chromosome consists of two sister chromatids connected at the centromere.

• From the centromere, the kinetochore captures spindle microtubules, which ensure that sister chromatid

• telomere→ at end

Other chromosome elements

• 1 or + origins of replication

• telomere at each end

Autosomes and sex chromosomes

• Karyotype: the number, size, and shape of the
  chromosomes

• Chromosomes are classified as sex chromosomes or
  autosomes

  • XX (female)

  • XY (male)

Why isn’t the introduced foreign plasmid DNA degraded by
a bacterial restriction-modification system?

Organization and expression of the genetic material

• Heterochromatin: chromatin that is condensed a suppresses transcription

• Euchromatin: chromatin that is more open and allows for gene activation

Eukaryotic gene expression is regulated at three levels

• DNA sequence: DNA-binding proteins associate with regulatory elements in the DNA.

• Chromatin structure: changes in the way the DNA is wrapped around the histones.

• Nuclear architecture: positioning of chromosomes in “territories” in the nucleus.

The majority of the eukaryotic genome is noncoding

Most genomic DNA consists of various classes of repetitive DNA sequences

Organization of the human genome

Less than 40% of the human genome is comprised of genes and gene-related sequences

Repetitive DNA sequences are divided into two major classes

• Interspersed elements (primarily transposable elements)

  • genome wide repeats made of degenerate copies of transposable elements

    • Short interspersed nuclear elements (SINEs)

    • Long interspersed nuclear elements (LINEs)

  • EX: AGAG………GAGA (has gaps)

• Tandem repetitive elements (Arranged in arrays with variable numbers of repeats)

  • 3 subdivisions based on length

    • Satellite DNA (1.69 density), (reg DNA 1.7)

      • Very highly repetitive DNA

      • Buoyant density during density gradient centrifugation differs from that of the bulk of the DNA.

      • lighter density bv they have a lot of AT (GC is heavier and more density)

    • Minisatellites

    • Short tandem repeats (STRs)

    • EX: AGAGAGAGAGAG (all right next to each other)

Lateral gene transfer in the eukaryotic genome (Graffith experiment)

• Lateral or horizontal transfer -> the transfer of DNA between two different species, especially distantly related species.

• Important mechanism for bacterial evolution; in particular, through movement of transposable elements.

Organelle genomes reflect an endosymbiont origin

• Mitochondria and chloroplast contain own genetic information (CpDNA & mtDNA)

• Endosymbiont Hypothesis: both organelles derived from primitive, free-living, bacterial- like organisms

Intercompartmental DNA transfer

• a type of lateral gene transfer

• associated with gradual loss of endosymbiont’s independence on the path to becoming an organelle

Eukaryotic genomes are mosaic

• made of complicated evolutionary history

• most human genes transferred from endosymbiont

  • proteins in nuclear envelope made of genes of both archael and bacterial origin

Prokaryotic and viral genome organization

bacterial genome organization

• single, covalently closed circular DNA molecule

• nucleoid: condensation involving histone-like proteins into a structure

Histone-like or nucleoid-associated proteins

• HU (heat-unstable protein)
• IHF (integration host factor)
• HNS (heat-stable nucleoid structuring)
• SMC (structural maintenance of chromosomes)

lateral gene transfer in bacteria

• source of genetic material for bacteria

• allows for rapid response to changing environments

Plasmid DNA

• Small, double-stranded circular or linear DNA molecules.
• Carried by bacteria, some fungi, and some higher plants.
• Extrachromosomal, independent, and self-replicating.
• Carriers of resistance to antibiotics.(gene in plasmid tht creates protein that resists antibiotics)
• Vehicles for genetic engineering.

independent and works seperate from baterial chromosomes

Archael genome organization

• One double-stranded circular DNA molecule (0.5 to 5.5 Mb)

• Some archaea have two distinct histones

Viral genome organization

• Bacteriophages (Prokaryotic viruses

  • Genome typically consists of a single DNA molecule, largely devoid of associated proteins

• Mammalian DNA viruses

  • infect mammalian cells and make use of host machinery for their replication and in Varity of diverse forms