Coding sequence array Office hours Wednesday 3 4pm 304A Stanley Hall Review session 5pm Thursday Dec 11 GPB100 Fig 1 13 RNA seq Expression effects of cancer AAAAA AAAAA AAAAA Solexa sequencing counts seq maps 26982 25885 17851 15715 14963 TCGTTCACTTGTATTGG TCTCTACTGGTGGTGGT GACAAACTGTCGCTGTC TCTCTACCGGTGGTGGT TCGTTCACTTGTAATGG 610 607 602 602 601 600 599 TTGAAGCTACCACCAAC TGTCCTTATCTATGTGT CGTACTTTTTTAATTGT ATCATTGTTCCAGAAAT TTATCAGAGGTGCTGGT CAAAGACCTCATTTAAT AGGAGGGTATATATGCT U0 U0 R0 U0 U0 genome pos sbaySum fsa chr03 fsa 3002121 138912 orient R F sbaySum fsa chr04 fsa 11182634 1489376 F R sbaySum fsa chr11 fsa 8491512 145622 R F chr14 fsa sbaySum fsa chr14 fsa 694435 4671591 575509 R R R R0 U0 U1 R0 U0 U0 U0 Diagnosis via transcriptional profile Diagnosis via transcriptional profile patient samples transcripts 1 Marker is linked to polymorphism in expression regulation cascade Linkage mapping of mRNA levels Black 6 mouse x DBA mouse G 111 F2 progeny kinase TF Microarray each F2 liver TF Genotype each F2 TF ORF G Looking for linkage coinheritance between marker and mRNA level G Locally acting polymorphisms Nonlocal polymorphisms 25 of varying mRNAs are caused by locally acting polymorphism Polymorphism responsible for mRNA difference is at the locus of the gene itself Nonlocal polymorphisms Clinical applications Black 6 mouse x DBA mouse 111 F2 progeny One polymorphism in a key regulator can affect a regulon 100 s of related mRNAs Microarray each F2 liver Genotype each F2 Measure fat pad each F2 2 Clinical applications Clinical applications Colored curves fat mass at different body locations Clinical applications Finding polymorphism responsible for difference in macroscopic phenotype is hard Clinical applications Finding polymorphism responsible for difference in macroscopic phenotype is hard If mRNAs change too can learn mechanism from known function of encoded proteins Clinical applications Clinical applications 3 Clinical applications Clinical applications Counts allele 1 allele 2 cases 1 5 Counts allele 1 allele 2 controls Clinical applications Clinical applications Marker predicts quantitative expression level association Linkage of human transcripts Can we map expression traits first disease afterward 4 Linkage of human transcripts Association of human transcripts Association of human transcripts Association in multiple populations linkage families assoc unrelated European Americans in Utah Han Chinese and Japanese Association in multiple populations A new brand of genetic variation 5 Translation Fig 8 25 Translation Fig 8 25 PSI yeast read through STOPs PSI yeast read through STOPs PSI yeast read through STOPs Weird genetics of read through Haploid PSI Haploid psi Diploid PSI 40 150 bp 6 Weird genetics of read through Haploid PSI Weird genetics of read through Haploid PSI Haploid psi Diploid PSI Haploid psi Diploid PSI sporulate Haploid PSI Haploid PSI Haploid PSI But why wouldn t it get diluted over many divisions sporulate Haploid PSI Cytoplasmic aggregates of Sup35 Haploid PSI Haploid PSI Haploid PSI Haploid PSI Cytoplasmic aggregates of Sup35 How would this explain the results Hard to make aggregate easy to join Protein inheritance 7 Protein inheritance PSI begets more PSI Original from PSI nucleates in all progeny Not due to dominant genetics in the usual way Nucleating prions in mad cow disease Is PSI the yeast analog of mad cow or Alzheimer s If bad would be lost If bad would be lost Pichia methanolica vs S cerevisiae 8 Genetically distinct S cerevisiae strains Genetically distinct S cerevisiae strains Genetically distinct S cerevisiae strains Genetically distinct S cerevisiae strains PSI phenotypes PSI phenotypes PSI phenotypes PSI phenotypes PSI phenotypes 50 C PSI phenotypes Why would aggregates result in so many novel abilities and traits 50 C 9 PSI phenotypes The clincher Why would aggregates result in so many novel abilities and traits Apparently does not happen in Alzheimer s The clincher partial LOF The clincher partial LOF What do you conclude A Sup35 does not cause resistance to paraquat B Prions do not cause resistance to paraquat C Aggregation is not necessary to cause resistance to paraquat D Aggregation is not sufficient to cause resistance to paraquat The clincher partial LOF The clincher partial LOF Aggregates per se don t cause resistance Aggregates per se don t cause resistance Losing function of sup35 does 10 Aggregation more read through Aggregation more read through New extra long forms of proteins cause new traits PSI allows epigenetic change in protein sequence Genetically distinct S cerevisiae strains Genetic effects Genetically distinct S cerevisiae strains Genetic effects Phenotypes varied between genetically diverse PSI strains Aggregation more read through Phenotypes varied between genetically diverse PSI strains How can the cause be genetic and non genetic protein aggregates at the same time 11 Aggregation more read through Aggregation more read through UTR mutations usually occur and have no effect UTR mutations usually occur and have no effect so organism doesn t die and allele is maintained Aggregation more read through Aggregation more read through UTR mutations usually occur and have no effect so organism doesn t die and allele is maintained Now in PSI they manifest Sequence differences in readthrough region cause phenotypic differences between PSI strains Cryptic variation DNA sequence differences between individuals that are usually not expressed 12
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