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The mating type locus Chr. III

The mating type locus Chr. III. The MAT locus information. The MAT locus can encode three regulatory peptides: - a 1 is encoded by the MAT a allele -  1 and  2 are encoded by the MAT  allele Three regulatory activities:  1,  2, and a 1-  2.

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The mating type locus Chr. III

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  1. The matingtype locusChr. III

  2. The MAT locus information • The MAT locus can encode three regulatory peptides: • - a1 is encoded by the MATa allele • - 1 and 2 are encoded by the MAT allele • Three regulatory activities: 1, 2, and a1-2.

  3. Sterile mutants can monitor the MAT status • Mutations have been identified at several loci that produce a non-mating phenotype, called sterile (STE). • The sterile mutations fall into three classes: • 1. sterility only in a cells • - STE2, the a pheromone receptor • 2. sterility only in  cells • - STE3, the  pheromone receptor • 3. sterility in both a and  cells • - STE12, the general pheromone-responsive transcription factor

  4. Saccharomyces as a model system • How do cells generate a mitotically stable, complex, specific cell type? •  same DNA, but different gene expression states. • How do cells respond to environmental change or information from other cells? • decision-making algorithms. • How do cells maintain an undifferentiated state “stem cell”? •  non-equivalence of daughter cells at mitosis.

  5. Sterile mutants can monitor the MAT status • The STE genes can be used to track the effects of mutations at other loci, such as MAT. • STE response be measured as fertility/sterility (mating). • Or, reporter gene constructs made with the transcriptional response elements from STE genes can drive the E. coli-galactosidase gene. • The reporter gene is visualized on screens by the ability to metabolize XGAL to a blue color, giving blue (gene active) or white (gene inactive) colonies. STE12 response b-galactosidase

  6. MAT regulation in  cells • When the  allele is present at MAT, two genes are expressed: MAT1 and MAT2, • Mutations in 1 affect only -specific genes, such as STE3. • MAT1 mutants prevent normal expression of STE3. • They do not affect other haploid specific genes or a-specific genes. •  1 is a positive regulator of -specific genes • Mutations in 2 allow the expression of a-specific genes, even in a MAT cell. • 2 is a negative regulator of a-specific genes • Consequently, in a MAT cell the  genes are expressed while the a genes are not.

  7. Genetic elements of yeast

  8. The yeastgenome • First eukaryotic genome sequenced, April 1996 • Consortium effort, US / EU • 16 well characterized chromosomes • PFGE separation of chromosomes • Chr. I (230 kb) <-> chr. IV (1532 kb) • 13 Mb (3.5 x coli) • 6183 ORFs > 99 aa • 72% coding ! (<2% human) • Average ORF 1450 bp • Few introns (<4% of ORFs) • 1/3 of ORFs characterized • 1/3 of ORFs have homologies, motifs • 1/3 of ORFs have unknown function • 120 rRNA copies of 9137 bp on chr. XII • 262 tRNAs

  9. Essential genes • About 1000 of the 6100 ORF are essential genes • Test for essential gene: • Gene disruption in diploid • Sporulation and tetrad dissection • 2 viable 2 dead spores • Many genes would be essential in nature that are dispensable on laboratory rich media • eg. carbon source • Temperature • Salts...

  10. The genetic and physical map of chromosome III  Both strands contain about the same number of ORFs  Often several ORFs on one strand not interrupted by ORFs on the other strand  Very few overlapping ORFs on the same strand  No overlap of divergently transcribed ORFs  Close shared promoters of divergently transcribed ORFs  Most DNA is ORF  Few and small introns  Genes close to the centromer

  11. chromosome III (cont.)  Dispersed tRNAs (270 / genome)  Ty elements and there remnants are 5’ to tRNAs  Dispersed snRNAs and snoRNAs  3kb / cM (200x less than in humans)  rRNA on Chr XII, no recombination, nucleolus remains associated with the chromosome during meiosis  Moderate suppression of recombination around centromeres  Genome 4300 cM -> 45 x 2 crossovers per meiosis

  12. Genetic nomenclature • 3 letter name with digit, eg. CDC33, CMD1 • Italic = genes • Uppercase = wild-type • Loss of function, cdc33 • cdc33-1, known allele • Cdc33 protein, Cdc33p • Phenotypes TS+, ts- • arg2∆,arg2::LEU2 • Dominant / recessive • ORF designation YCR49w

  13. The genome duplication • whole genome duplication 100 mio years ago (polyploidy; Ohno’s hypothesis, shark)  Tetraploid -> diploid + many deletions and reciprocal translocations • 55 duplicate regions, 13% of all ORFs, 50% of the genome ! • functions in anaerobiosis ?

  14. Genetic elements of yeast

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