gene & genome evolution1 chapter 9 you will not be responsible for: read the how we know section...
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Gene & Genome Evolution 1
Gene & Genome EvolutionChapter 9
You will not be responsible for:
Read the How We Know section on Counting Genes, and be able to discuss methodologies for doing so.
Questions in this chapter you should be able to answer:Chapter 9- #1 -7 , 9, 10 - 16, 18
Gene & Genome Evolution 2
How do genes evolve over time?
Mutation of coding regions
Mutation of regulatory regions
Chromosome/Gene/Exon duplications
Exon/intron shuffling & Transposition
Horizontal gene transfer
Gene & Genome Evolution 3
Exon duplication & shuffling is common
Gene & domain duplications occurred during evolution of the “Ig-Superfamily”
Exon shuffling &duplication has occurred duringevolution of these genes
Gene & Genome Evolution 4
Gene duplications are common
Divergence of function
e.g. Fetal/human hemoglobin
Families of related genes
Pseudogenes can result
Gene & Genome Evolution 5
Horizontal Gene Transfer-- can move blocks of genes
Asexual transfer of genes between organisms
Most common in single-celled organisms-- why?
Bacterial genetic recombination-- spread of Ab resistance
Gene & Genome Evolution 6
Simple mutations to regulatory genes can cause dramatic changes in development
Explains “Punctuated Equilibrium”
Mutations to “master regulatory gene”
Antennapedia (antp)-- antennae transformed to legs
bithorax (bx) + postbithorax (pbx)-- extra set of wings
Chromatin Structure and Replication 7
Trends in genome evolution
1) Accumulation of non-coding DNA
2) Accumulation of transposable elements
3) Loss of GC pairs
4) Intron Expansion
5) Accumulation of SNPs
Figures 9-32 & 9-33
Chromatin Structure and Replication 8
2) Accumulation Transposable elements
Alu – about 300 Bp-- 106 copies-- new Alu insert ~1/200 live births
L1 (Line) elements-- longer-- encode genes
reverse transcriptase& endonuclease
-- 5 x 105 copies
Many copies are “dead”
Can be disruptive-- cancers
Chromatin Structure and Replication 9
How do transposable elements move?
DNA-only mehanism-- common in bacteria, plants, yeast, insects
Inverted sequences
Mechanism of cut and paste transposition
Chromatin Structure and Replication 10
Alu and Li are retrotransposons
Pass through RNA form
Use reverse transcriptase
Transposable elements can move genes and exons
e.g., Antibiotic resistance genes
Gene & Genome Evolution 11
3) Loss of GC pairs Vertebrates
‘Cytosine methylation and gene regulation
CpG’ vs ‘GC’ bp
Methylation of CpG leads to loss of GC bp’s
Deamination of methyl-C yields T – G mismatch
Gene & Genome Evolution 12
Creation of CpG islands
CpG remains in ‘islands’
Where found?housekeeping genesnon-coding regions
FrequenciesGroup GC CpG Fish & amphibians 44% 1.8%Birds and mammals 42% 1.13% “GC-islands” 4-6% Jabbari, et al. 1997 Gene 205:109-118
Gene & Genome Evolution 13
4) Intron expansion
Genome sizesPuffer fish: 4 x 108
Human: 3 x 109
Huntingtin gene sizePuffer fish: 2.4 x 104
Human: 1.8 x 105
All 67 exons align!!
Expansion and mobile elements occur in introns
Gene & Genome Evolution 14
5) Accumulation of single-nucleotide polymorphisms (SNP)
distinguish individual genomes
Consequence of “point mutations”
107+ documented in humans
Can influence:Our individual physical traitsDisease susceptibilityRisk factors for disorders
e.g., Macular DegenerationSNP in Complement factor HHis Tyr5 – 7x >risk
Gene & Genome Evolution 15
What is a “silent mutation”?
Why are they not always silent?
Sometimes: Wobble positionNon-coding regions
Sometimes not:regulatory sites chromosome codon usage
Arginine tRNA occurrence
Codon tRNA [tRNA]1
CGU arg2 5.54CGC arg2 CGG arg3 1.45AGA arg4 2.64AGG arg5 1.611tRNA abundance in E. coli: Burg & Kurland (1997) J. Mol. Biol. 270: 5442Frequency in E. coli O127:H6 http://www.kazusa.or.jp/codon/
What would be the expected effect on translation rate of … … CGU CGC mutation? … CGU CGG mutation?