biosci d145 lecture 1 page 1 © copyright bruce blumberg 2004. all rights reserved organization and...
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![Page 1: BioSci D145 lecture 1 page 1 © copyright Bruce Blumberg 2004. All rights reserved Organization and Structure of Genomes (contd) Genome size –i.e. total](https://reader036.vdocuments.net/reader036/viewer/2022062518/5697bf811a28abf838c85640/html5/thumbnails/1.jpg)
BioSci D145 lecture 1 page 1 ©copyright Bruce Blumberg 2004. All rights reserved
Organization and Structure of Genomes (contd)
• Genome size– i.e. total number of DNA bp – Varies widely - WHY?
• C- paradox– i.e., what is the source of the
differences?• Do the number of genes required
vary so much?– (how many “phyla” are represented at
the right?)
Phylum Chordata
Phylum Arthropoda
![Page 2: BioSci D145 lecture 1 page 1 © copyright Bruce Blumberg 2004. All rights reserved Organization and Structure of Genomes (contd) Genome size –i.e. total](https://reader036.vdocuments.net/reader036/viewer/2022062518/5697bf811a28abf838c85640/html5/thumbnails/2.jpg)
BioSci D145 lecture 1 page 2 ©copyright Bruce Blumberg 2004. All rights reserved
Organization and Structure of Genomes (contd)
• How to measure genome complexity?– Hybridization kinetics– Shear and melt DNA– Allow to hybridize and measure ds
vs ss by spectrophotometry
• Cot½ - measures genome size and complexity– Larger value – longer to hybridize
• Smaller k– Longer to hybridize – more unique
sequences, larger genome– Much of what we knew about
genome size and complexity comes from these studies
![Page 3: BioSci D145 lecture 1 page 1 © copyright Bruce Blumberg 2004. All rights reserved Organization and Structure of Genomes (contd) Genome size –i.e. total](https://reader036.vdocuments.net/reader036/viewer/2022062518/5697bf811a28abf838c85640/html5/thumbnails/3.jpg)
BioSci D145 lecture 1 page 3 ©copyright Bruce Blumberg 2004. All rights reserved
Organization and Structure of Genomes (contd)
• Assumptions
– Cot½ measures rate of association of sequences
– Simple curves at right suggest simple composition
• No repetitive sequences• (graphed inverse to book)
• What would a more complex genome look like?– Would it be just shifted
further to the right?
– Or ?
![Page 4: BioSci D145 lecture 1 page 1 © copyright Bruce Blumberg 2004. All rights reserved Organization and Structure of Genomes (contd) Genome size –i.e. total](https://reader036.vdocuments.net/reader036/viewer/2022062518/5697bf811a28abf838c85640/html5/thumbnails/4.jpg)
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Organization and Structure of Genomes (contd)
• Measure eukaryotic DNA– Multiple components– Can calculate more than
1 Cot½ value
– Either means starting material is not pure (i.e., multiple types of DNA)
– Or means different frequency classes of DNA
• Highly repetitive• Moderately repetitive• Unique
– Very big surprise
![Page 5: BioSci D145 lecture 1 page 1 © copyright Bruce Blumberg 2004. All rights reserved Organization and Structure of Genomes (contd) Genome size –i.e. total](https://reader036.vdocuments.net/reader036/viewer/2022062518/5697bf811a28abf838c85640/html5/thumbnails/5.jpg)
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Organization and Structure of Genomes (contd)
• What does it mean?
Genetic complexity is not directly proportional to genome size!
• Increase in C is not alwaysaccompanied by proportionalincrease in number of genes– Note incorrect numbers
in chart• Drosophila
– ~14,000• human
– Controversial– ~30-50K
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Organization and Structure of Genomes (contd)
• What can we learn by hybridizing RNA back to the genomic DNA?– Label RNA and hybridize with
excess DNA – measure formationof hybrids over time
– Rot½ analysis shows that RNA doesnot hybridize with highly repetitive DNA
– What does this mean?• Most of mRNA is transcribed
from non-repetitive DNA• Moderately repetitive DNA is
transcribed• Highly repetitive DNA is
probably not transcribed into mRNA– Key argument why
genome sequencers do not bother with “difficult” regions of repetitive DNA
![Page 7: BioSci D145 lecture 1 page 1 © copyright Bruce Blumberg 2004. All rights reserved Organization and Structure of Genomes (contd) Genome size –i.e. total](https://reader036.vdocuments.net/reader036/viewer/2022062518/5697bf811a28abf838c85640/html5/thumbnails/7.jpg)
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Organization and Structure of Genomes (contd)
• Gene content is proportional to single copy DNA– Amount of non-repetitive DNA has a
maximum,total genome size does not– What is all the extra DNA, i.e., what is it
good for?
– Where did all this junk come from and why is it still around?
• Repetitive DNA• Telomeres• Centromeres• Transposons• Junk of all sorts
• DNA replication is very accurate• Selective advantage?
• OR
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Organization and Structure of Genomes (contd)
• What is this highly repetitive DNA?
• Selfish DNA?– Parasitic sequences that exist solely
to replicate themselves?
• Or evolutionary relics?– Produced by recombination,
duplication, unequal crossing over
• Probably both– Transposons exemplify “selfish DNA”
• Akin to viruses?
– Crossing over and other forms of recombination lead to large scale duplications
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Transcription of Prokaryotic vs Eukaryotic genomes
• Prokaryotic genes are expressedin linear order on chromosome– mRNA corresponds directly
to gDNA
• Most eukaryotic genes are interrupted by non-coding sequences– Introns (Gilbert 1978)– These are spliced out after
transcription and priorto transport out of nucleus
– Posttranscriptional processingin an important feature ofeukaryotic gene regulation
• Why do eukaryotes have introns?– What are they good for?
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Introns and splicing
• Alternative splicing can generate protein diversity– Many forms of alternative splicing seen– Some genes have numerous alternatively spliced forms
• Dozens are not uncommon, e.g., cytochrome P450s
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Introns and splicing
• Alternative splicing can generate protein diversity (contd)– Others show sexual dimorphisms
• Sex-determining genes• Classic chicken/egg paradox
– how do you determine sex if sex determines which splicing occurs and spliced form determines sex?
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Origins of intron/exon organization
• Introns and exons tend to be short but can vary considerably– “Higher” organisms tend to have longer lengths in both– First introns tend to be much larger
than others – WHY?
• Often contain regulatory elements– Enhancers– Alternative promoters– etc
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Origins of intron/exon organization
• Exon number tends to increase with increasing organismal complexity– Possible reasons?
• Longer time to accumulate introns?• Genomes are more recombinogenic due to repeated sequences?• Selection for increased protein complexity
– Gene number does not correlate with complexity– Ergo, it must come from somewhere
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Origins of intron/exon organization
• When did introns arise– Introns early – Walter Gilbert
• There from the beginning, lost in bacteria and many simpler organisms
– Introns late – Cavalier-Smith, Ford Doolittle, Russell Doolittle• Introns acquired over time as a result of transposable
elements, aberrant splicing, etc• If introns benefit protein evolution – why would they be lost?
– Which is it?
• Introns late(at the moment)
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Evolution of gene clusters
• Many genes occur as multigene families (e.g., actin, tubulin, globins, Hox)– Inference is that they evolved from a common ancestor– Families can be
• clustered - nearby on chromosomes (α-globins, HoxA)• Dispersed – on various chromosomes (actin, tubulin)• Both – related clusters on different chromosomes (α,β-globins,
HoxA,B,C,D)– Members of clusters may show stage or
tissue-specific expression • Implies means for coregulation as well
as individual regulation
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Evolution of gene clusters (contd)
• multigene families (contd)– Gene number tends to increase with
evolutionary complexity• Globin genes increase in number
from primitive fish to humans
– Clusters evolve by duplication and divergence
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Evolution of gene clusters (contd)
• History of gene families can be traced by comparing sequences– Molecular clock model holds that rate of change within a group is
relatively constant• Not totally accurate – check rat genome sequence paper
– Distance between related sequences combined with clock leads to inference about when duplication took place