Structural Genomics
Genetic Map
Based on recombination frequency
Launched???
1990
Focus
Study of gene products (mRNA, proteins)
Purpose
Compare genomes across species to understand evolution and gene function
Cytological Map
Chromosome apearance
Goal
Sequence all 3 BILLION bases by 2005
Techniques
Microarrays: Assess gene expression across the genome
GFP fusions: Visualize protein localization (also YFP,CFP,RFP)
Key Concepts
Homologs: Common ancestry
Paralogs: Same species, Gene duplication
Orthologs: Different Species, Same Function
Physical Map
DNA sequence overlap via restriction analysis
Key Playaaassss
COLLINS: Clone-by-Clone sequencing (HGP)
VENTER: Whole-Genome shotgun method (Celera)
Notes
mRNA doesn't fully reflect protein activity
Bioinformatics
Analyzes sequence data
Finds conserved exons, amino acids, and protein functions
RFLPs
(Restriction Fragment-Length Polymorphisms)
SNPs change DNA fragment lengths after enzyme digestion.
Useful as co-dominant genetic markers.
Results Published
Nature (HGP) - Feb 15, 2001
Science (Celera) - Feb 16, 2001
Notes part 2
Some functions inferred from protein structure similarity
VNTRs
(Variable Number Tandem Repeats)
Short sequences repeated in tandom
Used in genetic fingerprinting
Key Discoveries
~30,000-35,000 genes (less than expected)
BONUS how many where expected (__-__ expected)
Exons: 1.1% | Introns: 24% |Intergenic DNA:~75%
ENCODE project followed to study regulatory sequences