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Business
• Helpful video on translocations:
https://www.youtube.com/watch?v=WqHEndYJEkQ
• Homework due WEDNESDAY because of holiday
• Practice problems and sample exam on web site
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Roadmap
• One more deeply weird amphibian
• Selfish DNA:
– Repeated sequences
– Tranposable elements (transposons)
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Amphibian weirdness
• Pelophylax esculenta appears to be a species of water frog
• Originally a hybrid of P. ridibundus and P. lessonae
• It prefers to mate with P. lessonae
• Why doesn’t it get diluted out?
Pelophylax esculenta
(Rana esculenta)
Pelophylax ridibundus
(Rana ridibunda)
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Pelophylax lessonae
(Rana lessonae)
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Sexual and asexual lineages in the same species
• Like the triploid toads, P. esculenta has:
– A sexual, recombining part
– An asexual, nonrecombining part
• Will the asexual parts deteriorate over time?
• No examples known of diverse, old groups with genomes like this
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Selfish DNA
• How can a gene be “selfish”?
• Kinds of selfish DNA
– Meiotic drive (previously discussed)
– Repeats
– Transposons
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Selfish DNA
• Regular genes:
– Replicate only when genome replicates
– Increase their fitness by increasing organism’s fitness
– “Motivated” to work well with the rest of the genome
• Selfish genes (or genome regions):
– Replicate independently, or otherwise control their own reproduction
(t chromosome)
– Can increase their fitness without increasing organism’s fitness, by
making more copies of themselves
– Gene’s fitness is less dependent on working well with the rest of the
genome
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Examples of potentially selfish DNA
• Repetitive elements (microsatellites, etc)
• Transposons
• Meiotic drive loci (t chromosome)
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“Satellite DNA”
• Many repetitions of the same short
sequence
• In kangaroo rats, half the genome is AAG,
TTAGGG, CAACAGCGCGGG repeats
• First detected as peaks (“satellites”) in
DNA density
• Different GC content than the rest of the
genome
• Small localized groups of repeats are
“microsatellites”
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Satellite DNA: localized repeats
• Regions with satellite DNA are frequently in a condensed state called
heterochromatin
• Most active genes are inactivated if they are moved into
heterochromatin
• A few genes can remain active there
• Drosophila melanogaster heterochromatin patterns:
Mb
23.0
21.4
Mb
5.4 11.0
2R
Chromosome 2L
24.4
28.0
21.8
20.0
1.2
X
3L
8.2 8.2
Y
3R
40.9
Heterochromatin
Euchromatin
Centromere
X and Y
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3.1
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How does repeated DNA increase?
• Hard to duplicate repeats accurately:
– Replication slippage (same area gets replicated twice)
– Unequal crossing over
• Genetic drift can then cause copy number to increase or decrease
• Microsatellite rate of copy number change up to 10−4 per meiosis
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How does repeated DNA increase?
• Number of repeats cannot decrease below 1 by these mechanisms
• Mathematically, a random walk with a barrier in only one direction will
tend to move away from the barrier
• This might be kept in check by selection against the repeat:
– DNA replication is expensive
– Cells with lots of DNA divide slower and are larger
– One repeat more or less makes little difference!
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Function vs selfishness
• Does highly repeated DNA have a function? It might be involved in:
– Chromosome physical structure–spindle fiber attachment, etc
– Recognition of homologous centromeres
– Chromosome pairing
• Possible evidence for selfishness:
– Fitness in Drosophila is not reduced when heterochromatin is reduced
– Heterochromatin content varies widely between species
• Drosophila nasutoides has about 60% satellite DNA, but all on one
chromosome.
• Drosophila littoralis, D. ezoana have no satellite DNA
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Mobile elements
• Transposons can move or copy themselves into new genomic locations
• This can inactivate or truncate genes
• It can separate a gene from its usual promoter
• It can put a gene under control of the transposon promoter
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Mobile elements
• Conservative transposition:
– transposable element leaves its original position and moves to a new
position
– because of chromosome reassortment, can increase or decrease
genomic copy number
– can also increase copy number if transposition happens during DNA
replication (transposon replicates, moves, and replicates again)
– causes mutations which may cleanly revert when transposon leaves
– often a small duplication is left at the site
• Typical of most DNA transposons
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Mobile elements
• Replicative transposition:
–
–
–
–
transposon stays where it is; a new copy inserts elsewhere
increases copy number
causes mutations which do not easily revert
this can happen via DNA copying or via DNA to RNA reverse
transcription
– also tends to cause a small duplication at the site
• RNA transposons (retrotransposons) and some DNA transposons
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Heavy spotting shows activity of
Mu transposon
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Transposons as genome components
• Many transposon families have both active and inactive members
– Initial transposon codes for genes needed in transposition
– A copy can lose these genes but use proteins from other copies to
transpose
– Eventually copies deteriorate and stop transposing
• Within a genome, transposons evolve like organisms on their own
• However, if they evolve in ways contrary to host survival they die
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Transposons clog the human genome
• LINE elements
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–
–
–
–
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“Long interspersed elements”
Retrotransposons which code for a reverse transcriptase
Three families in humans (LINE1, LINE2, LINE3)
LINE1 is still active and can move
LINE2 and LINE3 have stopped transposing
LINEs have about 850,000 copies in human genome or 21% of
genome
• SINE elements
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–
–
–
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“Short interspersed elements”
Have lost the reverse transcriptase gene
Can transpose only in presence of related LINE
Alu family of SINEs is the biggest gene family in humans
SINEs have about 1,500,000 copies or 13% of genome
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Are retrotransposons viruses?
Two hypotheses:
• RNA virus from a retrotransposon:
– Cell evolved reverse transcriptase for its own use
– Transposon picked up a protein that could form a virus capsule and
became a virus
• Retrotransposon from an RNA virus:
– Virus infected cell and then lost ability to leave
– Reverse transcriptase now allows it to move within the cell
• Both of these may have happened at different times to different
viruses/transposons!
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Drosophilia P element transposon
• Found in wild D. melanogaster
populations
• Lab strains (started about 100 years
ago) lack P
• In wild flies:
– No transposition in somatic cells
– Rare transposition in germ line cells
• In wild x lab crosses:
– High transposition in all cells
– “Hybrid dysgenesis”–flies are sick
due to too much transposition
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Drosophilia P element transposon
Hypothesis: P element a new invasion of D. melanogaster
• Very similar P found in a distant relative (60 million years’ separation)
• Lab strains not only lack P, but lack suppressors to keep it from moving
• P may have come in via rare cross-species mating
• It spreads because it can move around in the genome
Drosophilia P element transposon
Transposition good or bad?
• If P truly spread across the world in 100-200 years, it’s clearly good–for
the transposon
• P moving in somatic cells kills the flies
• P moving at a high rate in germ cells is pretty bad too
• P-bearing strains experience strong selection for silencing of P
• P element can fight back by evolving immunity
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Evolutionary effects of transposons–discussion
• What would be different between a species with transposons and a
similar one without?
• Consider effects of:
– Mutations
– Similarity between different parts of the genome
– Genome size
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Thought problem
• Cross P into a lab strain and maintain a population in bottles
• Experimentally, population may live or die
• Which is likely to do better, a large or small population?
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Thought problem
• Cross P into a lab strain and maintain a population in bottles
• Experimentally, population may live or die
• Which is likely to do better, a large or small population?
• When this experiment has been done, large populations are more likely
to survive
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Genome shock hypothesis for transposons
• Barbara McClintock hypothesized that transposons allow an organism
to control its own mutation rate:
– Healthy vigorous plants suppress transposition
– Sickly plants allow transposition, leading to mutations which could
possibly be useful
– If you are sick already, you have little to lose and a lot to gain
• Alternative hypothesis: transposons are purely selfish
– Healthy vigorous plants suppress transposition
– Sickly plants aren’t able to do so because they’re too sick, so they are
vulnerable to transposition
• Not easy to test these alternatives
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One supportive observation
• Copia transposons in flies carry a heat-shock promoter
• Transposition is triggered when flies are stressed
• Hard to distinguish between:
– Heat-shock regulation of transposons helps the fly
– Heat-shock regulation of transposons helps the transposon
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Finding a use for transposons
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Oxytricha genome rearrangement
• Two nuclei per cell:
– Micronucleus used for reproduction, but genes not active
– Macronucleus expresses genes
• Macronucleus genome is highly rearranged:
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–
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Cut into around 16,000 tiny chromosomes
Mainly 1 gene per chromosome
Genes are re-assembled from fragments
Some are duplicated (dosage control?)
95% of germline genome is destroyed
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Transposons harnessed to chew
up genome
• Germline genome of Oxytricha full of
transposons
• Macronucleus has none
• If transposases are inactivated, the
macronucleus fails to develop properly
• Transposons and transposase probably
central in rearrangement process
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Other “tamed” genome rearrangements
• Vertebrate rearrangement of antibody genes
– Genome contains assortment of V, D and J segments
– Targeted rearrangement makes a final antibody gene
– This system greatly increases antibody diversity
• Yeast sex switching
– Genome contains inactive copies of a and α genes
– Targeted gene conversion allows sex switching
• Evolution can “use” elements which were initially selfish
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One-minute responses
• Tear off a half-sheet of paper
• Write one line about the lecture:
– Was anything unclear?
– Did anything work particularly well?
– What could be better?
• Leave at the back on your way out
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