 Yeast 15, 1775–1796 (1999) Systematic Analysis of S. cerevisiae Chromosome VIII Genes RAINER NIEDENTHAL 1 **†, LINDA RILES 2 †, ULRICH GU } LDENER 1 †, SABINE KLEIN 1 , MARK JOHNSTON 2 AND JOHANNES H. HEGEMANN 1 * 1 Institut fu ¨r Mikrobiologie, Heinrich-Heine-Universita ¨t Du ¨sseldorf, Universita ¨tsstrasse 1, Geb. 26.12.01.64, 40225 Du ¨sseldorf, Germany 2 Washington University, Medical School, Department of Genetics, Box 8232, 660 S. Euclid, St. Louis, MO 63110, U.S.A. To begin genome-wide functional analysis, we analysed the consequences of deleting each of the 265 genes of chromosome VIII of Saccharomyces cerevisiae. For 33% of the deletion strains a growth phenotype could be detected: 18% of the genes are essential for growth on complete glucose medium, and 15% grow significantly more slowly than the wild-type strain or exhibit a conditional phenotype when incubated under one of 20 different growth conditions. Two-thirds of the mutants that exhibit conditional phenotypes are pleiotropic; about one-third of the mutants exhibit only one phenotype. We also measured the level of expression directed by the promoter of each gene. About half of the promoters direct detectable transcription in rich glucose medium, and most of these exhibited only low or medium activity. Only 1% of the genes are expressed at about the same level as ACT1. The number of active promoters increased to 76% upon growth on a non-fermentable carbon source, and to 93% in minimal glucose medium. The majority of promoters fluctuated in strength, depending on the medium. Copyright  1999 John Wiley & Sons, Ltd.   — Saccharomyces cerevisiae; genome; functional analysis; gene deletion; homologous integration; green fluorescent protein GFP; FACS; phenotypic analysis; microtiter plate assays INTRODUCTION Knowledge of the genome sequence of the yeast Saccharomyces cerevisiae (Goffeau et al., 1996) allows us to imagine reaching the goal of describ- ing the function of all genes that specify this eukaryotic cell. This is a major challenge, because the sequence reveals that the majority of genes of this organism have resisted detection, despite many years of intensive investigation (Dujon, 1996; Garrels, 1996). To reach a complete under- standing of the structure and function of a yeast cell, the roles of these ‘occult’ genes must be revealed. Many of the previously hidden genes have prob- ably escaped detection because their inactivation does not cause phenotypes that geneticists have used to screen and select mutants. Previous com- prehensive genetic searches for mutants yielded only a minority of genes that exhibited one of the few phenotypes that was tested (Burns et al., 1994; *Correspondence to: Dr J. Hegemann, Institut fu ¨ r Mikro- biologie, Heinrich-Heine-Universita ¨t Du ¨ sseldorf, Universita ¨ts- strasse 1, Geb. 26.12.01.64, 40225 Du ¨ sseldorf, Germany. Tel.: (+49)-211-81-13733; fax: (+49)-211-81-13567; e-mail: hegemann@uni-duesseldorf.de **Present address: Institut fu ¨r Biochemie, Medizinische Hochschule Hannover, OE 4310, 30623 Hannover, Germany. †These authors contributed equally to this work. Contract/grant sponsor: McDonnell Foundation, U.S.A. Contract/grant sponsor: US National Center for Human Genome Research; Contract/grant number: HG00956. Contract/grant sponsor: FAZIT-Stiftung, Germany. Contract/grant sponsor: BMBF Project, Network for the func- tional analysis of unknown gene products, Germany; Contract/ grant number: FKZ 0310577. Contract/grant sponsor: EUROFAN Project of the EU. CCC 0749–503X/99/161775–22$17.50 Copyright  1999 John Wiley & Sons, Ltd. Received 30 April 1999 Accepted 10 August 1999