Yeast Pol II start‐site selection: the long and the short of it

Abstract

The formation of a pre‐initiation complex (PIC) is the first step that takes place during transcription by RNA polymerase II (Pol II). The TATA‐binding protein binds to the TATA box, thereby positioning the polymerase in the PIC in such a way that it can unwind downstream DNA and lock the template strand in the active site (Bushnell et al , 2004). In metazoans, initiation takes place 25–30 base pairs (bp) downstream of the TATA box (Smale & Kadonaga, 2003), whereas in Saccharomyces cerevisiae , start sites are spread across 40–120 bp downstream of the TATA box (Hampsey, 1998). The rules that control selection of the Pol II start point are not well understood. In metazoans, start sites often occur at a conserved initiator sequence (Smale & Kadonaga, 2003), whereas yeast initiators are more divergent (Zhang & Dietrich, 2005) and the polymerase has been proposed to ‘scan’ the downstream sequences for optimal start sites (Giardina & Lis, 1993; Kuehner & Brow, 2008). Several articles recently published by the Brow, Lacroute, Libri and Reines laboratories show that start‐site selection has an important role in regulating the expression of genes of the S. cerevisiae nucleotide‐biosynthetic pathways (Jenks et al , 2008; Kuehner & Brow, 2008; Kwapisz et al , 2008; Thiebaut et al , 2008). IMD2 and URA2 encode the initial enzymes in the pathways that lead to the synthesis of GTP and UTP, respectively. The transcription of these genes is repressed by the end product NTP (Escobar‐Henriques & Daignan‐Fornier, 2001; Losson & Lacroute, 1981); however, despite years of searching, no repressors or activators have been identified. Studies on IMD2 identified a guanine‐responsive TATA box and a repressive element spanning the messenger RNA (mRNA) start site, yet how these cis ‐elements regulate IMD2 expression was unclear (Escobar‐Henriques et al , 2003; …