Promoter architectures in the yeast ribosomal expression program

Abstract

Ribosome biogenesis begins with the orchestrated expression of hundreds of genes, including the three large classes of ribosomal protein, ribosome biogenesis and snoRNA genes. Current knowledge about the corresponding promoters suggests the existence of novel class-specific transcriptional strategies and crosstalk between telomere length and cell growth control.

Figure 1

Organization of typical RP, ribi and snoRNA gene promoters in Saccharomyces cerevisiae. The consensus sequences reported on the right (M, A or C; W, A or T; R, A or G; Y, C or T; K, G or T; N, any nucleotide) are based on the following references: Rap1, IFHL,, Abf1,,, RRPE and PAC,, Reb1,, and Tbf1.,, The reported distances are with respect to the TSS (right-pointing arrow). Boxes with a thinner border indicate sequence elements occurring in a minority of promoters within each set. Poly(dA:dT) indicates either poly(dT) or poly(dA) stretches on the coding DNA strand, that prevail in RP and snoRNA promoters, respectively.

Figure 2

Upstream TF binding sites in ribi gene promoters. (A) GeneDoc visualization of Clustal X alignments of orthologous promoter regions from different Saccharomyces genomes for the ribi genes ARX1 (YDR101C) and RRP7 (YCL031C). ce, S. cerevisiae; pa, S. paradoxus; mi, S. mikatae; ba, S. bayanus; ku, S. kudriavzevii. Schematics of promoter organization are shown under the alignments. The reported distances are with respect to the TSS, while the alignments also include 5′-UTR sequences. (B) Tbf1 binding sites upstream of snoRNA-associated ribi genes. Schematics of promoter organization are shown. The reported distances are with respect to the TSS (right-pointing arrow). Introns are indicated by a simple line, with intron-located snoRNA genes as cyan boxes. The lengths of the first exons of IMD4 and TEF4 are not to scale.