Thu, 21 Aug 2008 01:20:58 BST CiteULike: gpalidwor's Giuliodori http://www.citeulike.org/user/gpalidwor/author/Giuliodori CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/gpalidwor/article/2109972 <i>J Mol Biol, Vol. 333, No. 1. (10 October 2003), pp. 1-20.</i><br /><br />Transcription of eukaryotic tRNA genes relies on the TFIIIC-dependent recruitment of TFIIIB on a approximately 50 bp region upstream of the transcription start site (TSS). TFIIIC specifically interacts with highly conserved, intragenic promoter elements, while the contacts between TFIIIB and the upstream DNA have long been considered as largely non-specific. Through a computer search procedure designed to detect shared, yet degenerate sequence features, we have identified a conserved sequence pattern upstream of Saccharomyces cerevisiae tDNAs. This pattern consists of four regions in which particular sequences are over-represented. The most downstream of these regions surrounds the TSS, while the other three districts of sequence conservation (appearing as a centrally located TATA-like sequence flanked by T-rich elements on both sides) are located across the DNA region known to interact with TFIIIB. Upstream regions whose sequence conforms to this pattern were found to potentiate tRNA gene transcription, both in vitro and in vivo, by enhancing TFIIIB binding. A conserved pattern of DNA bendability was also revealed, with peaks of bending propensity centered on the TATA-like and the TSS regions. Sequence analysis of other eukaryotic genomes further revealed the widespread occurrence of conserved sequence patterns upstream of tDNAs, with striking lineage-specific differences in the number and sequence of conserved motifs. Our data strongly support the notion that tRNA gene transcription in eukaryotes is modulated by composite TFIIIB binding sites that may confer responsiveness to variation in TFIIIB activity and/or concentration. A composite upstream sequence motif potentiates tRNA gene transcription in yeast. S Giuliodori R Percudani P Braglia R Ferrari E Guffanti S Ottonello G Dieci J Mol Biol, Vol. 333, No. 1. (10 October 2003), pp. 1-20. 2007-12-14T02:28:28-00:00 2003 J Mol Biol 0022-2836 333 1 1 20 no-tag http://www.citeulike.org/user/gpalidwor/article/2109865 <i>J Mol Biol, Vol. 299, No. 3. (9 June 2000), pp. 601-613.</i><br /><br />The most peculiar transcriptional property of eukaryotic tRNA genes, as well as of other genes served by RNA polymerase III, is their complete dependence on the intragenic interaction platform provided by transcription factor IIIC (TFIIIC) for the productive assembly of the TBP-containing initiation factor TFIIIB. The sole exception, in yeast, is the U6 RNA gene, which is able to exploit a TATAAATA element, 30 bp upstream of the transcription start site, for the TFIIIC-independent assembly of TFIIIB. To find out whether this extragenic core promoter organization and autonomous TFIIIB assembly capacity are unique features of the U6 gene or also apply to other genes transcribed by RNA polymerase III, we scanned the 5'-flanking regions (up to position -100) of the entire tRNA gene set of Saccharomyces cerevisiae searching for U6-like TATA motifs. Four tRNA genes harboring such a sequence motif around position -30 were identified and found to be transcribed in vitro by a minimal system only composed of TFIIIB and RNA polymerase III. In this system, start site selection is not at all affected by the absence of TFIIIC, which, when added, significantly stimulates transcription by determining an increase in the number, rather than in the efficiency of utilization, of productive initiation complexes. A specific TBP-TATA element interaction is absolutely required for TFIIIC-independent transcription, but the nearby sequence context also contributes to the efficiency of autonomous TFIIIB assembly. The existence of a TFIIIB assembly pathway leading to the faithful transcription of natural eukaryotic tRNA genes in the absence of TFIIIC provides novel insights into the functional flexibility of the eukaryotic tRNA gene transcription machinery and on its evolution from an ancestral RNA polymerase III system relying on upstream, TATA- centered control elements. TFIIIC-independent in vitro transcription of yeast tRNA genes. G Dieci R Percudani S Giuliodori L Bottarelli S Ottonello doi:10.1006/jmbi.2000.3783 J Mol Biol, Vol. 299, No. 3. (9 June 2000), pp. 601-613. 2007-12-14T02:12:25-00:00 2000 J Mol Biol 0022-2836 299 3 601 613 no-tag