Questions for Chapter 17 and 18:

1
Questions for Chapter 17 and 18 17 4, 7,
10, 13 18 2 3
2
Comparing Genomes
What are the major genomic differences between
prokaryotes and eukaryotes?
Size E. coli - 4.64 x 106 bps for 4,397
genes S. cerevisiae - 12 x 106 bps for 6,548
genes H. sapiens - 3.3 x 109 bps for
30-35,000 genes
Organization prokaryotes - tend to have 1
circular chromosome - many operons - no
introns, and little repetitive DNA eukaryotes
- multiple linear chromosomes - few operons,
some genes within genes - introns common,
repetitive DNA common
3
Comparative Organization of DNA
4
Highly Repetitive DNA

• Satellite DNA
• highly repetitive DNA found in genome -
  pericentric
• VNTRs used for DNA finger printing
• Centromere DNA
• highly conserved DNA maintains
  chromosome structure
• Telomere DNA
• GGGGTTA in Tetrahymena and GGGATT in
  Humans
• highly conserved

etc
5
Transposon-Derived Repeats
Most human repeat sequence is derived from
transposable elements
6
Repetitive Transposed Sequences
Sequence that can move about the genome
Short Interspersed Elements (SINES) less than
500 bp but 1,500,000 copies in the human genome
best characterized is the Alu family
Long Interspersed Elements (LINES)
bigger than SINES best example is
the L1 family 6400 bp in length and present up
to 100,000 copies per genome LTR
retrotransposons retrovirus-like elements
DNA transposons
7
Chromatin Organization
What do you get when you put all of these
components together?
8
Chromosomes
G-banding
9
Evolution of Genomes
?
E. Coli 4.64 Mbps 4,397 genes
H. sapien chromosome 22 - 33.4 Mbps
545 genes 134 pseudogenes
10
Evolution of Genomes
11
Evolution of Genomes
Genomic duplication and gene duplication
12
http//www.ornl.gov/hgmis/publicat/primer/intro.ht
ml
http//www.nature.com/genomics/human/papers/articl
es.html
13
Types of Mapping

• Genetic linkage map
• linear description of markers/genes on a given
  chromosome with markers closer being inherited
  together more often.
• Physical Map
• The physical location on the chromosome - two
  types - Cytogenetic and physical

14
Comparison of Genetic Maps
Gene or Marker
Gene or Marker
Genetic Linkage Map
Restrction Fragments
Contig Library
DNA Sequence
15
Linkage Mapping
A genetic linkage map shows the relative
locations of specific genes and DNA markers along
the chromosome. Any inherited physical or
molecular characteristic that differs among
individuals and is easily detectable in the
laboratory is a potential genetic marker.
16
Cytogenetic Mapping

• Cytogenetic map or a physical map
• Several levels of physical mapping
• -Chromosome, chromosome arm, band specific
  
• region within an arm, or a certain
  stretch of bases

Karyotype
In situ hybridization
17
Macrorestriction maps Top-down mapping

• A single chromosome is cut (with rare-cutter
  restriction enzymes) into large pieces, which are
  ordered and subdivided.
• The smaller pieces are then mapped further.
  The resulting macro-restriction maps depict the
  order of and distance between sites at which
  rare-cutter enzymes cleave.

18
Contig Maps Bottom-up Mapping

• The bottom-up approach involves cutting the
  chromosome into small pieces, each of which is
  cloned and ordered. The ordered fragments form
  contiguous DNA blocks (contigs).

• Contig maps consist of a linked library of
  small overlapping clones from a complete
  chromosomal segment

19
Advantages of Contig Maps

• An advantage of this approach is the
  accessibility of these stable clones to other
  researchers.
• Useful for finding genes localized to a small
  area (under 2 Mb).
• Technological improvements now make possible
  the cloning of large DNA pieces, using
  artificially constructed chromosome vectors that
  carry DNA fragments (BACS, YACS).

20
Ultimate Map
DNA sequence is the ultimate map!
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Uses for Gene Mapping

• Find genes (quantitative trait loci) that are
  associated with traits of economic importance.
• Use genetic markers for marker assisted
  selection.
• Discover genes causing major physiological
  defects.
• Develop comparative maps.

22
Comparative Genome Mapping
synteny on the same chromosome