Chromosome III of Saccharomyces cerevisiae: An ordered clone bank, a detailed restriction map and analysis of transcripts suggest the presence of 160 genes

Abstract

Using lambda phage vector EMBL4, we isolated 344 clones containing segments of chromosome III of Saccharomyces cerevisiae, analysed their physical structure with eight restriction enzymes and sorted the data in contiguous groups with computer programmes. Furthermore, we performed Southern hybridizations between the sorted contiguous clone groups and interrelated them into larger groups. In this way, we constructed an ordered clone bank that covers almost the whole of chromosome III with a single gap of several kilobases in length. The consensus physical map thus obtained totals 334.6 kb, which is in good agreement with the size of this chromosome estimated by pulsed-field gel electrophoresis. Southern hybridization analysis with the DNA probes containing telomere-specific sequences showed that the bank contained a telomere at a position corresponding to the right arm terminus of chromosome III. Also, five Ty elements were found to be present. To estimate the number of genes on this chromosome and to analyse their levels of expression, we performed a series of Northern hybridization experiments using total poly(A)+ RNA from vegetatively growing cells and appropriate restriction enzyme fragments from the bank. Thus, we identified a total of 156 transcripts on chromosome III, indicating, on an average, one gene in every 2 kb on this chromosome. The transcripts were visually categorized into five groups according to their apparent levels of expression. It was found that the genes located near both termini are expressed only at low levels and that highly expressed genes are rather scattered over the chromosome.

Membrane protein retrieval from the Golgi apparatus to the endoplasmic reticulum (ER): characterization of the RER1 gene product as a component involved in ER localization of Sec12p.

“…In our hands, for example, the distance between the LEU2 and the MAT loci on the chromosome III was only 21 cM, much shorter than the value of 48 cM in the genetic map (Mortimer et al, 1989). There is a hot spot of Ty transposon insertion on the right arm near the centromere of this chromosome (Yoshikawa and Isono, 1990), which might have affected the recombination frequency. Due to this anomaly, we spent a long time identifying the RERI locus, which was finally found between the LEU2 locus and this hot spot.…”

“…We decided to take advantage of this genetic information to isolate the RER1 gene. An ordered clone bank covering all of the chromosome III was Molecular Biology of the Cell available (Yoshikawa and Isono, 1990), and the whole nucleotide sequence of the chromosome III had been determined (Oliver et al, 1992). Six ordered clones (1D2, 4B11, 3E10, 3A12, lFll, and 3E11), which contain a continuous region from the PGK1 through the CRYI loci on the chromosome III, were obtained from Isono's collection and subjected to subcloning into the single copy plasmid pRS314 (Figure 2).…”

“…EMBL4 A phage vectors containing the ordered clones of the yeast chromosome III (Yoshikawa and Isono, 1990) …”

“…structed on a A phage vector (Yoshikawa and Isono, 1990 (Nakano et al, 1988;d'Enfert et al, 1991) and A RERlIpSHF9-4 rer1-2fpSHF9-4/pRS31 4 rerl-2IpSHF9-4IpRS314RER1-X rerl-2IpSHF9-4IpRS314RER1-3HA Figure 10. The RERI-3HA gene complements the rerl-2 mutation.…”

Clustering of meiotic double-strand breaks on yeast chromosome III

“…2) and therefore the absence of DSBs in the cold domains is not due to an unusually low gene density. The levels of chromosome III transcripts have been studied systematically in vegetative cells and ranked from level 1-5 (most expressed) (31). We observe that the transcript levels in both telomeric domains (I and V) are biased toward the low levels (rank 1-2) but the internal domains with DSBs (II, IV) and without DSBs (III) have a similar pattern (ranking 2-4).…”