Download Alu - Environmental

Using an Alu Insertion
Polymorphism to study
Human Populations
Human Genome
• How many chromosomes does each human cell
have?
• 22 pairs of autosomal chromosome and 1 pair of sex
chromosomes
• What is the size of the human genome?
• The human genome is made up of 3 billion base pairs
• How many genes does the Human Genome code for?
Genome Comparison
Organism
# of Genes
Genome Size (bp)
E.coli
4,200
4,600,200
S. cervisiae (yeast)
6,000
12,000,000
C. elgans (nematode)
14,000
100,000,000
D. melanogaster (fruit fly)
14,000
140,000,000
A. thaliana (mustard plant)
24,000
120,000,000
20,000-25,000
3,000,000,000
Mammalian
Human Genome
• What is a gene?
• A gene is segment of a genome that encodes a single specific end
product (a protein or RNA) or a functional unit or information
• How much of the genome are “genes”?
• ~1.5% of the genome
• What accounts for the rest of the DNA in the genome?
Human Genome
• Other items in genome
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Introns
Repeated sequences (telomeres, centromeres)
Non-coding RNAs
Transposons (SINES and LINES)
Psuedogenes (genes that no longer produce functional products)
Alu elements
• http://www.geneticorigins.org/pv92/aluframeset.htm
• Under media/animations
• Illustrations about the Alu element listed as How Alu jumps
• Pedigree on Alu inheritance listed as PV92 inheritance
Alu elements
• Alu is a “defective” transposon of the SINE (Short INterspersed
Element) family
• Alu is about 300 nucleotides (base pairs) in length
• Human chromosomes have more than 1 million Alu copies (10% of
the genome by mass)
• There is no evidence that an Alu can be lost from a site – it can only
be inserted
Alu elements
• Alu has the necessary sequences to be transcribed by RNA Pol III
• The LINE (Long INterspersed Element) L1 supplies the reverse
transcriptase needed for Alu to jump
• L1 is a defective retrovirus
• It nicks the DNA close to the sequence AATTTT
• The AAAA of Alu transcript binds to the TTTT of the nicked DNA – the
acts as a primer for the L1 to bind to
Alu Elements
• What are the consequences and benefits of having an Alu element?
• Alu inserting into exons has been implicated in neurofibromatosis,
cancer and heart attacks
• They can provide alternate splicing in 5% of genes which leads to
genetic diversity
• Can provide information on migration and evolution
Alu elements
• Alu elements are only found in the primate branch
• Each Alu insertion is a unique event and is inherited
from each parent
• Most occurred millions of years ago and are often on both
pairs of chromosomes
• There are Alu elements that have occurred since humans
branched from other primates
• This gives rise to dimorphic Alus from the last hundreds of
thousands of years
• Estimated to jump 1:200 live human births
Alu Elements
• The Alu element that we will be looking at in on chromosome 16
• There is no phenotypic data associated with this locus (i.e. does not
associate with disease, trait, or sex determination)
Alu Lab
• What is the benefit of saline? Why not mouth swabs?
• Saline is a very reproducible way of harvesting cells – it loosens a large
number of single cheek cells
• Cheek swabs harvest much larger clumps of cells that are not lysed as
efficiently when boiling
• What about food contamination?
• No effect because the element is only found in primates
• Why are we boiling the samples?
• To lyse open the cells and release the DNA
• What is Chelex?
• Chelex is a metal binding resin
• It is used to scavenge metal that can contaminate PCR reactions
Alu Lab
• Where do the primers amplify?
• Primers amplify region on chromosome 16 – outside of the Alu region –
the primers do not amplify Alu itself
• What will the products (+/+, +/- and -/-) look like?
• -/- has one smaller band around 400bp, +/+ has one larger band around
700bp; +/- has two bands one at 400 and one at 700
• There is a picture of a control gel on:
http://www.geneticorigins.org/pv92/aluframeset.htm under the theory
section
• Why is there no control for the PCR reaction?
• There is no need for a control because all samples will produce a band
therefore it will tell us if the DNA was good without a need for an
additional control
Alu Lab
• Waiver form
• Possible problems
• Highly complicated lab 1 mistake results in inconclusive results
• Lose cell pellet at the beginning
• No amplification
• Maybe didn’t get complete lysis
Alu within the Alu
Alu paper is on the wiki listed under PCR lab DNA Polymorphism: Recent
Insertion of an Alu element within a Alu insertion
Online alignment tool
• http://www.ch.embnet.org/software/LALIGN_form.html
• To use Alignment tool copy the mutated large Alu sequence into the box
labeled 1st query sequence
• Make sure to name the sequence in box labeled First sequence title (I named this
Mut)
• Paste Alu element (non-mutated) sequence into box labeled 2nd sequence
query
• Make sure to name the sequence in box labeled Second sequence title (I named this
Alu)
• Click Run Align at the bottom of the page
• This will produce the alignment with the details about what bases were
aligned and the % of identity
• This will give you three alignments with the Alu element
Alu within the Alu
Mutated larger Alu sequence (from GenBank extension number
AF302689):
aactgggaaa atttgaagag aaagtcacac agatacattt cagtaaggtt gtctctgtta
61 cttgaggctt acaagaagga aagaaggccg ggcgcggtgg ctcacgcctg taatcccagc
121 actttgggag gccgaggcgg gcggatcacg aggtcaggag atcgagacca tcccggctaa
181 aacgctgaaa cctcgtctct actaaaaata caaaaaattg ccgggcgcgg tggctcacgc
241 ctgtaatccc agcactttgg gaggccgagg cgggtggatc atgaggtcag gagatcgaga
301 ccatcctggc taacaaggtg aaaccccgtc tctactaaaa atacaaaaaa ttagccgggc
361 gcggtggcgg ggcgcctgta gtcccagcta ctcgggaggc tgaggcagga gaatggcgtg
421 aacccgggaa gcggagcttg cagtgagccg agattgcgcc actgcagtcc gcagtccggc
481 ctgggcgaca gagcgagact ccgtctcaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa
541 aaaaaaaaaa aaaataccaa aaattagccg ggcgtagtgg cgggcgcctg tagtcccagc
601 tacttgggag gctgaggcag gagaatggcg tgaacccggg aggcggagct tgcagtgagc
661 cgagatcctg ccactgcact ccagcgtggg cgacagagcg agactccgtc tcaaaaaaaa
721 aaaaaaaaaa aaaaaaagaa agaattccct ctctaaacac actctaacac acaggagttg
781 agaactca
Alu within the Alu
Alu sequence (non-mutated):
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggcggatcacgaggtcaggagat
gagaccatcccggctaaaacgctgaaacctcgtctctactaaaaatacaaaaaattagccgggcgtagtggcgggcgctgtagtccca
gctacttgggaggctgaggcaggagaatggcgtgaacccgggaggcggagcttgcagtgagccgagatcctgccactgcactccagc
ctgggcgacagagcgagactccgtctcaaaaaaaaaaaaaaaaaaaaaaaaaaa
Alu within the Alu
Alu within the Alu:
sequence results
½ Alu sequence
Full Alu sequence
½ Alu sequence
Website
National Geographic articles on using the Y-chromosome to trace migration
out of Africa
http://news.nationalgeographic.com/news/2002/12/1212_021213_journeyof
man.html
DNA interactive website: links to Human Identification, Recovering the
Romanovs, Human Origins and Genes and Medicine
http://www.dnai.org/d/index.html