The identification of transcriptional start sites (TSSs) in pombe. Schizosaccharomyces pombe 972h-

To elucidate how Tor1 and Tor2, two TOR isoforms, oppositely regulate gene expression of amino acid permeases in S. pombe, we have employed the cap analysis of gene expression (CAGE), a method of analyzing expression profiles and identifying transcriptional start sites (TSSs) in prototrophic tor2-287 mutant and tor1 knockout cells. The library was subjected to 50-base single read sequencing on a HiSeq 2000 sequencer. The sequencing generated 10 to 20 million reads from each sample. The reads with low-quality and ambiguous bases and corresponding to ribosomal RNA were removed using fastX tool kit, respectively. The remaining reads were mapped to S. pombe reference genome using bwa. CAGE read clustering, differential gene expression analysis and motif discovery were performed by RECLU ver3.1 pipeline.