Download Human Genome - iPlant Pods

“Jumping Genes” Lead The Way
Uwe Hilgert, UofA
iPlant, BIO5 Institute & CDTIS
[email protected]
A bioinformatics/biotech workshop
at the
AZCTE Conference 2015
Research & Teaching
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PCR
Agarose gel electrophoresis
Electronic PCR
Sleuth genetic relationships
Navigate NCBI
DNA Subway
Hardy-Weinberg
Population Genetics/Allele Server
Simulation Server
Biology
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Human migration
Polymorphisms and alleles
Random genetic drift vs. selective pressure
DNA amplification
Mobile genetic elements
Bioinformatics
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Access sequence databases
Conduct sequence searches
Perform electronic PCR
Explain the various types of sequence searches
Retrieve sequences
Align sequences
Analyze sequences
Determine sequence relationships
Interpret gene and genome maps
Identify Genetic variation
Workshop Goodies
Stuff
• Agenda:
https://goo.gl/Df1T6f
• Repository: https://goo.gl/Df1T6f
• Etherpad: https://goo.gl/VNcA3a
People
• Lead:
• First TA:
• Second TA:
• Organizer:
[email protected]
[email protected]
[email protected]
[email protected]
Human Genome
• Human genome:
– 25% protein-coding genes
– 3% protein-coding sequence
– 50% repetitive DNA
25% Alu and Line (L1) retro-transposons
• Other
– Corn: 75% Transposons
– Lily: 98% Transposons
• Animation
– Chr 11 Flyover
Iris brevicaulis
Transposons
• Mode of transposition
– Excise and Insert (Transposons, Transposase
protein)
– Copy and Paste (Retroposons, Reverse
Transcriptase protein)
• Structure
– Central: Genes for “mobility proteins”
– Flanking: Mobility protein action sites (repeats)
• Level of independence
– Have genes & flanks  can jump by own volition
(Line, Ac)
– No genes; flanks ok  can be jumped (Alu, Ds)
– Genes, flanks faulty  can jump others
How do organisms live with TEs?
• Most TEs are broken (cannot tranpose; “fossils”).
• Active TEs evolved to insert into “safe-havens.”
• Host regulates TE movement.
• “Stress” conditions may activate TEs.
• TEs can provide advantages.
Transposable elements can shake up otherwise conservative
genomes and generate new genetic diversity.
TEs can alter gene expression
Can this have phenotypic consequences?
Nipponbare
EG4
EG4 is salt tolerant
Whose Ancestor?
• Mom + Dad DNA
• “Blood” relatives share DNA
• PV92 locus/site in human
genome
• Exists in different form/alleles
• Alternative allele arose about
100,000 years ago
• No selection
• Simulation Server
Whose Ancestor?
PV92 Wetlab
• Cheek-cell DNA
• PCR
• Agarose gel
• Personal
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“Blood” relatives share DNA
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PV92 locus/site in human genome
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Exists in different forms/alleles
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Alternative allele arose about 100 kya
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No selection
PV92 eLab
• ePCR
• PV92 locus/site
• PV92 in humans
• Species (Specia-l)
Workshop Goodies
Stuff
• Agenda:
https://goo.gl/Df1T6f
• Repository: https://goo.gl/Df1T6f
• Etherpad: https://goo.gl/VNcA3a
People
• Lead:
• First TA:
• Second TA:
• Organizer:
[email protected]
[email protected]
[email protected]
[email protected]