Coding sequence array Office hours Wednesday 3-4pm 304A Stanley Hall

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1 Coding sequence array Office hours Wednesday 3-4pm 304A Stanley Hall Review session 5pm Thursday, Dec. 11 GPB100 Fig RNA-seq Expression effects of cancer AAAAA AAAAA AAAAA Solexa sequencing counts seq maps TCGTTCACTTGTATTGG TCTCTACTGGTGGTGGT GACAAACTGTCGCTGTC TCTCTACCGGTGGTGGT TCGTTCACTTGTAATGG TTGAAGCTACCACCAAC TGTCCTTATCTATGTGT CGTACTTTTTTAATTGT ATCATTGTTCCAGAAAT TTATCAGAGGTGCTGGT CAAAGACCTCATTTAAT AGGAGGGTATATATGCT R0 genome pos sbaysum.fsa chr03.fsa orient R F sbaysum.fsa chr04.fsa F R sbaysum.fsa chr11.fsa R F chr14.fsa sbaysum.fsa chr14.fsa R R R R0 U1 R0 Diagnosis via transcriptional profile Diagnosis via transcriptional profile patient samples transcripts 1

2 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 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

3 Colored curves = fat mass at different body locations Finding polymorphism responsible for difference in macroscopic phenotype is hard Finding polymorphism responsible for difference in macroscopic phenotype is hard If mrnas change too, can learn mechanism from known function of encoded proteins 3

4 Counts allele 1/allele 2, cases Counts allele 1/allele 2, controls = 1.5 Marker predicts quantitative expression level = association Linkage of human transcripts Can we map expression traits first, disease afterward? 4

5 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

6 Translation Translation Fig Fig 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 bp 6

7 Weird genetics of read-through Weird genetics of read-through Haploid PSI+ Haploid psi- Haploid PSI+ Haploid psi- Diploid PSI+ sporulate Diploid PSI+ sporulate But why wouldn t it get diluted over many divisions? Haploid PSI+ Haploid PSI+ Haploid PSI+ Haploid PSI+ Haploid PSI+ Haploid PSI+ Haploid PSI+ Haploid PSI+ Cytoplasmic aggregates of Sup35 Cytoplasmic aggregates of Sup35 How would this explain the results? Hard to make aggregate, easy to join Protein inheritance 7

8 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

9 Genetically distinct S. cerevisiae strains Genetically distinct S. cerevisiae strains Genetically distinct S. cerevisiae strains Genetically distinct S. cerevisiae strains 50 C Why would aggregates result in so many novel abilities and traits?? 50 C 9

10 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

11 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? Phenotypes varied between genetically diverse PSI+ strains. Genetic effects? Aggregation = more read-through Genetically distinct S. cerevisiae strains Phenotypes varied between genetically diverse PSI+ strains. How can the cause be genetic and non-genetic (protein aggregates) at the same time? 11

12 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