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Lecture 8

Biology 1001A Lecture 8.pdf

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Biology 1001A
Beth Mac Dougall- Shackleton

Biology 1001A | 2012 LECTURE NOTES Lecture 8: Origins of Variation –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– List of Mechanisms to Generate Genomic Diversity. - mobile elements - SNPs (single nucleotide polymorphisms) - CNVs (copy number variations) - transposons (both jumping and copying) - retrotransposons How much variation is there? - Venter individual genome sequence showed 1.2 million variants▯ - 25% of variant bases are SNPs (single nucleotide polymorphisms) - 75% of variant bases are CNVs (copy number variations) - each person has about 1000 CNV affecting 35% of genes - genome projects are revealing that we are more different than we thought - each person has about 300 variants in insertion of retro elements (LINES, SINES) Mobile Elements - mobile elements (things in you genome that move around) are very significant sources of variation - think about your genome as an ecosystem, where it is inhabited by mobile elements - bacterial elements code for their own mobility (transposases) - the insertion sequence codes for its own mobility, it moves around inside a genome - if there is an insertion sequence on both sides of a central sequence, then the entire sequence can be moved at the same time–this is called a transposon - many transposons carry genes for antibiotic resistance, allowing them to move around in and between organism, this is common in bacteria as a means of transferring antibiotic resistance - some elements move with, some without, making a copy, therefore they “jump” from one location to another, however these elements do not actually “jump” because this recombination event occurs with the sequence always in contact with DNA strands - other elements move by sending a copy of themselves elsewhere - both of these mechanisms create variation - retrotransposons move by first making an RNA copy of the DNA sequence via transcription, followed by reverse transcription of the RNA strand into a DNA strand by reverse transcriptase and finally the retrotransposon is integrated into the DNA at another point - retrotransposons are a way of making copies of genes - retroviruses form a large part of the genome - sometime in evolution, an ancestor was infected by a retrovirus - the virus was mutated so that it could not create a protein coat, therefore it cannot leave and is stuck in the genome Biology 1001A | 2012 - Alu elements cause disease, they are the retroviruses that are stuck in the gene and disrupt the function - what evidence or data would help you determine how long your human genome has been inhabited by a given mobile element? - how many times that it appears in your genome - look at species that are related to us and see if they have the element, then use the points at which the species diverged to estimate the age of the element - mobile elements can be very active in plants, and therefore plants good for investigating mobile elements SNPs (Single Nucleotide Polymorphisms) - populations from Africa have many more unique, novel SNPs than any other group - a given pair of African people are likely far more diverse that two people of other different races are from each other - populations from Africa have many more novel SNPs than any other population - where do SNPs come from? - mutations arise from perfectly natural processes inherent in the instability of the chemistry - SNPs are the result of spontaneous tautomeric shifts which change base
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