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Transcript of Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on...
![Page 1: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/1.jpg)
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
![Page 2: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/2.jpg)
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
![Page 3: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/3.jpg)
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
![Page 4: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/4.jpg)
Gene & Genome Evolution 4
Gene duplications are common
Divergence of function
e.g. Fetal/human hemoglobin
Families of related genes
Pseudogenes can result
![Page 5: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/5.jpg)
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
![Page 6: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/6.jpg)
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
![Page 7: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/7.jpg)
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
![Page 8: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/8.jpg)
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
![Page 9: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/9.jpg)
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
![Page 10: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/10.jpg)
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
![Page 11: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/11.jpg)
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
![Page 12: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/12.jpg)
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
![Page 13: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/13.jpg)
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
![Page 14: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/14.jpg)
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
![Page 15: Gene & Genome Evolution1 Chapter 9 You will not be responsible for: Read the How We Know section on Counting Genes, and be able to discuss methodologies.](https://reader036.fdocuments.in/reader036/viewer/2022062422/56649ec15503460f94bccb07/html5/thumbnails/15.jpg)
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?