Complete Transcriptional Map of Yeast Chromosome XI in Different Life Conditions G.-F. Richard, C. Fairhead and B. Dujon* Unite  de Ge Âne Âtique Mole Âculaire des Levures (URA1149 du CNRS and UFR927 U. P.M. Curie, Institut Pasteur 25 rue du Dr Roux, F-75724 Paris cedex 15, France Systematic sequencing of the genome of Saccharomyces cerevisiae has demonstrated the existence of many novel genes, whose functions need to be studied. Entire chromosome sequences also offer the possibility to examine functional properties of the genome at a higher hierarchical level than the genes themselves. We used ordered DNA fragments of chromo- some XI to systematically probe yeast DNA and total RNA extracted from MAT a, MAT a and diploid cells grown under three different con- ditions. Taking into account transcript sizes and uniqueness of probes, we attributed 94 transcripts to sequence-predicted open reading frames (ORFs) or tRNA genes; another 83 being tentatively assigned. The remaining 187 ORFs on chromosome XI do not correspond to transcripts detected under our conditions. More than 80% of transcripts are constitu- tively expressed, others are regulated by medium composition or cell type, the most frequent regulations being determined by carbon source (glycerol/glucose) or rich versus synthetic medium. Moreover, we show that transcript levels and regulation patterns are not statistically different between ORFs of unknown function, which constitute ca. 40% of the total, and previously identi®ed genes (ca. 30%) or their structural homo- logues. # 1997 Academic Press Limited Keywords: Saccharomyces cerevisiae; transcript map; duplications; chromosome analysis; gene regulation *Corresponding author Introduction The yeast Saccharomyces cerevisiae is the only eukaryotic organism whose genome is entirely sequenced (Goffeau et al., 1996). It has a small (13,389 kb) and compact genome (one gene every 2 kb on average). Few genes contain introns and repetitive elements are rare. Many new genes have been discovered from the sequence, a large fraction of which have no predictable function in the ab- sence of homologues in sequence data banks. At this stage, direct experimental approaches are needed to determine their function. Massive re- verse genetics techniques can now be applied to yeast genes in search for phenotypes, but several converging studies will be needed to obtain a com- plete picture of gene properties. Among those, pro- tein pro®les or gene fusion approaches can be used to determine gene expression. Transcript maps offer the most direct approach to gene expression studies. They can con®rm the existence of genes predicted only from the sequence and which could have no detectable phenotype when deleted. They can reveal the existence of additional genes. Finally, they allow a global vision of transcription patterns along a chromosome. Systematic tran- script maps of chromosomes III, VI and of parts of chromosome I were established before sequencing of these chromosomes (Coleman et al., 1986; Steensma et al., 1987; Yoshikawa & Isono, 1990; 1991; Tanaka & Isono, 1993; Barton & Kaback, 1994). In addition, a major interest of a transcript map is to detect regulation patterns, which allow classi®cation of novel genes. We have analysed total RNA extracted from cells under different life conditions, using a set of DNA probes that cover almost all of chromosome XI (5% of the yeast genome). Because duplications of sequences occur in the yeast genome, Fairhead & Dujon (1994) included systematic probing of Southern blots of genomic DNA in a pilot study on two regions of chromosome XI. We now report re- sults of the same strategy applied to the whole of chromosome XI. Abbreviations used: ORF, open reading frame; LTR, long terminal repeat; PCR, polymerase chain reaction. J. Mol. Biol. (1997) 268, 303±321 0022±2836/97/170303±19 $25.00/0/mb970973 # 1997 Academic Press Limited