The mating type locus Chr III The MAT

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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: -

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

Sterile mutants can monitor the MAT status • Mutations have been identified at several

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 - STE 2, the a pheromone receptor 2. sterility only in cells - STE 3, the pheromone receptor 3. sterility in both a and cells - STE 12, the general pheromone-responsive transcription factor

Saccharomyces as a model system • How do cells generate a mitotically stable, complex,

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.

Sterile mutants can monitor the MAT status • The STE genes can be used

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. STE 12 response b-galactosidase

MAT regulation in cells • When the allele is present at MAT, two genes

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 STE 3. • MAT 1 mutants prevent normal expression of STE 3. • 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.

Genetic elements of yeast

Genetic elements of yeast

– First eukaryotic genome sequenced, April 1996 – Consortium effort, US / EU –

– 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 r. RNA copies of 9137 bp on chr. XII – 262 t. RNAs The yeast genome

Essential genes • About 1000 of the 6100 ORF are essential genes • Test

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. . .

The genetic and physical map of chromosome III Both strands contain about the same

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

chromosome III (cont. ) Dispersed t. RNAs (270 / genome) Ty elements and there

chromosome III (cont. ) Dispersed t. RNAs (270 / genome) Ty elements and there remnants are 5’ to t. RNAs Dispersed sn. RNAs and sno. RNAs 3 kb / c. M (200 x less than in humans) r. RNA on Chr XII, no recombination, nucleolus remains associated with the chromosome during meiosis Moderate suppression of recombination around centromeres Genome 4300 c. M -> 45 x 2 crossovers per meiosis

Genetic nomenclature • • • 3 letter name with digit, eg. CDC 33, CMD

Genetic nomenclature • • • 3 letter name with digit, eg. CDC 33, CMD 1 Italic = genes Uppercase = wild-type Loss of function, cdc 33 -1, known allele Cdc 33 protein, Cdc 33 p Phenotypes TS+, tsarg 2∆, arg 2: : LEU 2 Dominant / recessive ORF designation YCR 49 w

The genome duplication • whole genome duplication 100 mio years ago (polyploidy; Ohno’s hypothesis,

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 ?

Genetic elements of yeast

Genetic elements of yeast