Biology 1001A Lecture Notes - Lecture 8: Single-Nucleotide Polymorphism, Retrotransposon, Insertion Sequence

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Published on 16 Nov 2012
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LECTURE NOTES
Lecture 8: Origins of Variation
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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
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