The major promoter element of rRNA transcription in yeast lies 2 kb upstream

Characterization of the region around the start point of transcription of ribosomal RNA in the Chinese hamster

The initiation site for ribosomal RNA transcription in the Chinese hamster was identified and the sequence around and upstream determined. The start point region shows considerable homology with comparable regions in the mouse and rat. In the Chinese hamster, the region between bp -700 and -200 consists of imperfect repeats approximately 120-130 bp in length which are flanked by T-rich regions. The region within each repeat which is homologous with an adjacent repeat decreases in length as the start point is approached. The final promoter-proximal repeat preserves only an 11-bp region of the promoter-distal repeats. This short sequence, termed the repeat core, appears with a periodicity of about 120-130 bp in the Chinese hamster, and is conserved in both mouse and rat. In humans, a short repeated sequence occupies similar positions, suggesting that while complete 120-130-bp repeats are not a feature of all mammalian RNA polymerase I promoter-proximal r X DNA spacers, a short sequence repeating with approximate 120-130-bp periodicity may be such a feature.

Primary structure of the maltase gene of the MAL6 locus of Saccharomyces carlsbergensis

We have determined the complete nucleotide (nt) sequence of a 2937-bp DNA fragment containing the yeast maltase (EC 3.2.1.20) gene (MAL6S) as well as part of the contiguous maltose permease gene (MAL6T) from the MAL6 locus of Saccharomyces carlsbergensis. The MAL6S gene encodes an alpha-glucosidase that is required for the utilization of maltose as a carbon source by yeast. The 5' transcription initiation sites for both MAL6S and MAL6T were determined by primer extension experiments using reverse transcriptase. The sequence data show one major open reading frame (ORF) of 584 amino acids (aa) for maltase with a calculated Mr of 68 107, somewhat larger than the value of 63 000 previously determined by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) analysis. The nucleotide sequences upstream of both the MAL6S and MAL6T genes, which are divergently transcribed, show common structural features for the transcription initiation of yeast genes as well as signals required for their translation. The codon bias index shows that the MAL6S gene is moderately expressed. The possible significance of two 17-bp dyad symmetric sequences, found in the intergenic region of MAL6S and MAL6T, for the control of expression of these genes is also discussed.

Upstream activation of ribosomal RNA biosynthesis in Saccharomyces cerevisiae

Yeast was transformed with eight recombinants that contained an rRNA minigene and upstream elements of rDNA in different orientations in the multi-copy yeast-Escherichia coli shuttle vector, pJDB207. The effect of these elements of upstream rDNA on the initiation of transcription of the minigene at the site for rRNA biosynthesis was determined by using an S1 nuclease mapping procedure to measure the abundance of the minigene transcript in RNA from the yeast transformants. Transcription of the minigene was enhanced 3-fold by DNA within a 2.2 kb element more than 1.5 kb upstream from the initiation site. Inversion of the 2.2 kb element decreased expression of the minigene by 40%. This 2.2 kb element contained approx. 500 bp from the 25S rRNA coding region at the 3' end of the preceding rRNA gene and 1 kb of adjacent nontranscribed spacer rDNA. The enhancing activity was independent of interference from readthrough that might have contributed to the 7-fold decrease in minigene expression caused by removing all rDNA upstream from -209 bp.

Heterogeneity in the ribosomal RNA genes of the yeast Yarrowia lipolytica; cloning and analysis of two size classes of repeats

Southern blotting of DNA from the ascomycetous yeast Yarrowia lipolytica revealed two major size classes of DNA units coding for rRNAs, which differ in length by about 1000 bp. We have cloned an rDNA unit of each size class. R-looping experiments revealed that the rRNA genes of both units are uninterrupted; subsequent heteroduplex analysis showed that the size difference both units is located within the nontranscribed spacer. Sequence analysis revealed that a major part of these spacers consists of a complex pattern of repetitions in periodicities of up to about 150 bp and that the difference between both rDNA units are located mainly in this repetitive region. Apart from different lengths of the repetitive regions, both rDNA units also reveal extended microheterogeneity within their homologous parts. Furthermore, no gene for 5S rRNA was observed in the spacer region. Therefore, the organization of the spacer of Yarrowia rDNA is clearly different from that of Saccharomyces cerevisiae.

Deletion mapping of the yeast Pol I promoter

Deletions in the promoter region of the 37S pre-rRNA operon in yeast were constructed and analysed in vivo using an artificial ribosomal minigene present on an extrachromosomal yeast vector. Sequences required for correct transcription initiation were found to be located between positions -192 and +15 relative to the start; a 5'-deletion down to position -133 reduces the transcription yield of the minigene at least five-fold. To allow detection of transcription of the minigene in isolated nuclei of yeast transformed with a minigene-bearing plasmid we attempted to increase the minigene copy number. The transcription yield in vivo appeared not to be proportional to the copy number but was found to be greatly enhanced when two or three minigenes are present in tandem. alpha-Amanitin sensitivity of transcription of these minigenes in isolated nuclei proved that RNA polymerase I is responsible for their transcription.