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Lecture 13

Biology 2581B Lecture 13: Lecture 13 genetics 2581

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Biology 2581B
David R Smith

Lecture 13  Chromosomal rearrangements can occur on a large and small scale and include: o Deletions o Insertions o Invesions o Duplications o Translocations o Reciprocal translocation o Whole genome duplication  Mouse versus human genome - at the sequence level they’re very similar and they have the same types of genes and their genes have similar sequences o However, at the chromosome level, when you compared the staining patterns of the chromosomes, there was no conservation suggested  But the mouse chromosome could be pieced together from putting together different human ones  Syntenic Segments:  Identity of genes  Order of genes  Orientation of transcription → almost the same: so basically they have the same types of genes, order and even their order of transcription is relatively the same, but they’re in different locations  You can take different genomes from grass and then line up the chromosomes as circles and you can see how they align - there are very few gaps o Can co-align them but there also has to be rearrangements occurring o Those occur over long stretches of time and also, only the ones that are not lethal are represented since only those rearrangements are sustainable  They have different time frames and different restrictions  Collinearity  Rearrangements can occur all the time and they’re not always deleterious since they actually lead to the generation of antibodies  Many antibodies generated  Mutations that occur on chromosome 14 and they’re involved in B cell development  In those rearrangements, you can bring segments together but in doing so, you would lose the segments in the middle  If there is a lack of diversity in the making of these antibodies, you can have a shift in the formation of T and B cell clones o Observed in lymphomas o You’re not generating the variants you need - making a diverse array of molecules is critical for a person’s health Deletions:  Loss of sequences  Small deletions affect a single gene  Large deletions lead to the loss of 10s or 100s of genes  Can be caused by X-ray or other chromosomal damaging agents that break the DNA backbone (X-rays break both strands of DNA) o Need two breaks and then you can lose the intermediate material  Most deletions are lethal but there are exceptions  Wolf-Hirschhorn Syndrome o Deletion from the short arm of chr4  Cri du Chat syndrome o Deletion from the short arm of chr5  Humans cannot survive if more than 3% of their genome is deleted  Most deletions are also dosage dependent - more or less of a particular product is important o Some genes need to have the correct dose in order to have no associated phenotype  Eg. Drosophila: a deletion in the notch gene leads to notches in the wing and even heterozygotes have some sort of phenotypic effect on the wing pattern, but they can still fly  No recombination can occur within a deletion loop since the genes in the loop cannot be separated → genetic distance between loci on either side will be underestimated o If you’re heterozygous and there is a deletion, then you cannot align between the two homologues since you’re sticking out like a loop o So even if you try to use recombination to figure out the distances between the loci, you cannot use a recombination event if there is a deletion loop  If you do mapping events, your estimates for the mapping distance will be wrong Detection of Deletions through PCR:  If you have sequence information, you can use PCR primers upstream and downstream of the deletion and you have a wild type PCR product and a deletion PCR product o By running the sample on the gel, you can look at the size differences o Can easily track if an individual is homozygous or heterozygous of alleles Detection of Deletions through Karyotyping:  For large deletions - can use dyes to see which part of the chromosomes are missing Using Deletions to Map Mutations  Drosophila o Polytene chromosomes in their salivary glands o Giant chromosomes  You make a huge array of chromosomes and the homologues stay together and they make giant chromosomes o Undergo 10 rounds of replication but no mitosis → each chromosome consists of 2 = 1024 double helices o So you’re increasing the number of chromosomes but they’re not separated into different cells o You can easily stain and visualize the chromosomes o Polytene chromosomes are oversized chromosomes which have developed from standard chromosomes and are commonly found in the salivary glands of Drosophila melanogaster o Similar sequences are close together and they will intercalate with the dye in a similar manner o You can see the deletion loops when you stain with these dyes o Some of these deletions are so big you can see which bands are affected and which loci o There are deletions that lead to changes in eye morphology o These loci were known to be relatively close together on the x chromosome but we’re not sure how far apart they are so we used deletions to map o Polytene chromosomes collect mutants and deletions and they can be identified very easily → can carry a lot of lines that carry different types of deletions in that particular area of that chromosome and you can collect and make a huge database and figure out what pieces are missing (which band patterns)  And then if you have an idea of where it is, you can order different deletions strains and then you’ll know which band patterns are missing  A deletion cannot be where you still have a wild type phenotype and you can use deletion mutants to compare and by doing so, you can look for phenotypes and decide which areas correlate to particular mutations Seb’s notes for this slide:  All 3 loci are in close pr
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