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Alu Human Polymorphism. How many chromosomes does each human cell have? –22 pairs of autosomal chromosome and 1 pair of sex chromosomes What is the size.

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Presentation on theme: "Alu Human Polymorphism. How many chromosomes does each human cell have? –22 pairs of autosomal chromosome and 1 pair of sex chromosomes What is the size."— Presentation transcript:

1 Alu Human Polymorphism

2 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? Human Genome

3 Genome Comparison Organism# of GenesGenome Size (bp) E.coli4,2004,600,200 S. cervisiae (yeast)6,00012,000,000 C. elgans (nematode)14,000100,000,000 D. melanogaster (fruit fly)14,000140,000,000 A. thaliana (mustard plant)24,000120,000,000 Mammalian 20,000-25,0003,000,000,000

4 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

5 Other items in genome –Introns –Repeated sequences (telomeres, centromeres) –Non-coding RNAs –Transposons (SINES and LINES) –Psuedogenes (genes that no longer produce functional products) Human Genome

6 Under media/animations –Illustrations about the Alu element listed as How Alu jumps –Pedigree on Alu inheritance listed as PV92 inheritance Alu elements

7 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

8 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

9 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

10 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

11 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 Elements

12 Online resources for mapping genetic diseases s/sloozeworm/scenario.cfm s/sloozeworm/scenario.cfm s/pedigree/mapgene.cfm s/pedigree/mapgene.cfm Human Genome

13 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

14 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: 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

15 Waiver form Possible problems –Lose cell pellet at the beginning –No amplification Maybe didn’t get complete lysis Alu Lab

16 Alu paper is on the wiki listed under Human DNA Polymorphism: Recent Insertion of an Alu element within a Alu insertion Online alignment tool To use Alignment tool copy the mutated large Alu sequence into the box labeled 1 st 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 2 nd 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

17 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

18 Alu sequence (non-mutated): ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggcggatcacgaggtcaggagat gagaccatcccggctaaaacgctgaaacctcgtctctactaaaaatacaaaaaattagccgggcgtagtggcgggc gctgtagtcccagctacttgggaggctgaggcaggagaatggcgtgaacccgggaggcggagcttgcagtgagcc gagatcctgccactgcactccagcctgggcgacagagcgagactccgtctcaaaaaaaaaaaaaaaaaaaaaaa aaaa Alu within the Alu



21 Alu within the Alu: sequence results Full Alu sequence ½ Alu sequence

22 National Geographic articles on using the Y- chromosome to trace migration out of Africa 212_021213_journeyofman.html DNA interactive website: links to Human Identification, Recovering the Romanovs, Human Origins and Genes and Medicine Website

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