Genome Organisation II

1
Genome Organisation II

• Eukaryotic genomes are completely different in
  their organisation compared to prokaryotic, and
  also much bigger
• Their genes are mostly split into exons and
  introns
• It is not certain which came first in evolution -
  genes with introns/exons or genes without
• Exons may allow evolution of proteins in a
  modular way

2
Eukaryotic chromosomes

• In metaphase of mitosis, chromosomes can be seen
  under microscope - they have a compact rod-like
  structure
• The ends of chromosome are called telomeres,
  function is to protect the ends of the DNA
• Near the middle is the centromere, function is to
  attach to spindles during cell division and
  ensure correct segregation
• Telomeres and centromeres contain special DNA
  sequences and associated proteins
• Telomeres are replicated differently from the
  rest of the genome - see figure 26.37 in
  Lehninger
• Different regions of the chromosome can be
  stained with dyes (e.g. Giemsa) giving a
  characteristic banding pattern

3
Eukaryotic chromosome structure
Genes, repeated sequences, replication origins
(mostly euchromatin)
Centromere (heterochromatin)
Telomeres (heterochromatin)
(Figure 24-3 Lehninger)
4
The problem of telomere replication
5
Telomere replication
6
Centromeres

• The centromere is essential for correct
  segregation of chromosomes during cell division,
  by attachment to spindles
• Centromere consists of a small, core DNA sequence
  (AT rich) and specific proteins
• In many species (e.g. humans) this is flanked by
  100s of copies of a tandemly-repeated sequence

7
Unique and repeated DNA

• If eukaryotic DNA is melted and allowed to
  re-anneal, it does so in 3 distinct phases
• The explanation is that there is highly
  repetitive DNA (which re-anneals quickly),
  moderately repetitive DNA (intermediate) and
  unique or single copy DNA (re-anneals slowly)

8
DNA melting
9
Classes of DNA

• Mammalian DNA contains 3 main classes of DNA
  sequence, as measured by Cot curves
• Highly repeated DNA (up to 1 million copies)
• Moderately repeated DNA (up to 100,000 copies)
• Unique sequence DNA (strictly speaking 1 copy,
  but in practice this also includes sequences with
  only a few copies)

10
Origins and function of DNA classes

• Highly repetitive
• Bits of old virus genomes
• Simple sequence repeats e.g. CACACA.
• Special sequences such as centromeres
• Moderately repetitive
• Other old virus genomes
• Multi-gene families, e.g. ribosomal RNA
• Single-copy
• Most normal genes

11
Types of repeated DNA
12
Ribosomal RNA genes
13
DNA fingerprinting

• An application of repeated DNA sequences found in
  mammalian genomes
• Highly variable between individuals
• No 2 people are the same, except identical twins

14
Disease caused by a repeat DNA sequence

• Mutations in the low-density lipoprotein receptor
  gene (LDLR) are a common genetic cause of heart
  disease due to hypercholesterolemia.
• The LDLR gene is 45kb long with Alu
  (highly-repetitive class) repeats in its introns.
  Recombination between 2 of these leads to a
  truncated gene and defective protein.

15
CpG islands

• But there are short (1-3kb) stretches rich in C,
  G, CG without methylation

• Vertebrate DNA has not much CG because it is
  mostly methylated and mutates to TG...

16
CpG islands

• CpG islands are found at 5 ends of many genes
• Unlike rest of genome they do not bind the MeCP2
  protein
• MeCP2 acts as a general repressor of transcription