Biology 4 Lecture - Genomes (Ch 21)
© copyright 2009 Marta D. de Jesus
I. How are genomes sequenced?
A. 3-step process
cytogenetic map
linkage map
physical map
B. Whole genome shotgun approach (pioneered by J. Craig Venter)
sequenceable pieces
vectors
sequence
II. How is this information accessed?
A. Databases
GenBank, EMBL & DNA Database of Japan
B. Programs
BLAST
C. genomics & proteomics
D. systems biology
E. compared
molecular evolution
distant species
ribosomal RNA genes
transcription factors
FOXP2
between members of a species
a. SNPs
b. copy number
1) microsatellites
Dr. Ken Jones on Apr 15, 09 - Bio 31
2) genes
III. Genome comparison
A. vary by size
1. prokaryotes
viruses
2. eukaryotes
B. vary by # of genes
1. prokaryotes
2. eukaryotes
3. mismatch!
4. helping to account for
IV. Eukaryotic non-protein coding DNA
A. codes for exons
B. repetitive DNA
transposable elements & related sequences
transposon vs. retrotransposon
Alu elements
Barbara McClintock (1940s; Nobel Prize 1983)
transposable elements
a. promote recombination
b. change
c. modify
d. change
6. other repetitive DNA
a. large-segment duplication
b. simple sequence
http://www.vivo.colostate.edu/hbooks/genetics/medgen/dnatesting/satellites.html (edited)
1) satellites are very highly repetitive
(i) repeat lengths of one to several thousand base pairs.
(ii) typically are organized as large (up to 100 million bp !) clusters in
the heterochromatic regions of chromosomes, near centrosomes and telomeres
(iii) these are also found abundantly on the Y chromosome.
2) minisatellites are moderately repetitive
(i) tandemly repeated arrays of moderately-sized (9 to 100 bp, but
usually about 15 bp) repeats
(ii) generally involving mean array lengths of 0.5 to 30 kb.
(iii) found in euchromatic regions of the genome of vertebrates, fungi
and plants and are highly variable in array size.
(iv) most highly polymorphic sequence elements yet discovered in the
human genome, and delineating the repeat lengths of these loci
is the basis of most DNA typing systems used in forensic
medicine.
3) microsatellites = simple sequence repeats (SSR) = short tandem repeats
(STR) = variable number tandem repeats (VNTR) are moderately
repetitive:
(i) arrays of short (2-6 bp) repeats found in vertebrate, insect and plant
genomes of arrays 10-100 bp long.
(ii) classified according to length as (mono-), di-, tri-, tetra-, penta-,
and hexanucleotide repeats.
(iii) human genome contains at least 30,000 microsatellite loci located
in euchromatin.
(iv) copy numbers are characteristically variable within a population
so used for population genetics studies (forensics, paternity
analysis, wildlife management, etc.)
4) In general, satellite DNAs show exceptional variability among individuals,
particularly with regard to the number of repeats at a given locus.
C. other non-coding DNA
1. introns & regulatory sequences
2. unique non-coding DNA
V. Genes
multigene families
1. eg: ribosomal RNAs
2. eg: - & - globin genes
contributing to genome evolution
1. mutation
2. duplications
3. multiple copies
pseudogenes
4. exon shuffling
D. comparing in development: Evo-Devo
1. homeotic genes
2. in metazoans:
Hox genes
homeobox
homeodomain
3. in plants
flower development
major master set is Mads-box