A common sequence motif involved in selection of transcription start sites of Arabidopsis and budding yeast tRNA genes

The transcription start site (TSS) is useful to predict gene and to understand transcription initiation. Although vast data on mRNA TSSs are available, little is known about tRNA genes because of rapid processing. Using a tobacco in vitro transcription system under conditions of impaired 5′ end processing, TSSs were determined for 64 Arabidopsis tRNA genes. This analysis revealed multiple TSSs distributed in a region from 10 to 2 bp upstream of the mature tRNA coding sequence (− 10 to − 2). We also analyzed 31 Saccharomyces cerevisiae tRNA genes that showed a smaller number but a broader distribution (− 13 to − 1) of TSSs. In both cases, transcription was initiated preferentially at adenosine, and a common ‘TCAACA’ sequence was found spanning the TSSs. In plant, this motif caused multiple TSSs to converge at one site and enhanced transcription. The TATA-like sequence upstream of Arabidopsis tRNA genes also contributed to TSS selection.