title: Hybridization array technology coupled with chemostat culture: Tools to interrogate gene expression in Saccharomyces cerevisiae.
abstract: Hybridization array technology is increasingly being used for the analysis of gene expression in the yeast Saccharomyces cerevisiae. It is a powerful technique in which the relative abundance of all the mRNA molecules transcribed under a particular condition may be simultaneously measured. However, most studies performed using this technique are carried out in batch culture where the growth rate and environment are continuously changing. Often, the experimental condition being studied also impacts on the growth rate of the cells. Changes in growth rate affect the pattern of gene expression. Consequently, the analysis and interpretation of experimental results obtained in this way are inherently problematic due to the difficulty in discriminating between effects due to the experimental condition per se and concomitant growth rate-related effects. Here, we present a method that addresses this problem by exploiting chemostat culture, in which the cells can be grown at a fixed growth rate, in combination with hybridization array technology. We use two experimental examples to illustrate the advantages of using this approach and then describe a specific application of this approach to investigate the effect of carbon and nitrogen limitation at the transcriptome level.
authors.affiliation: School of Biological Sciences, University of Manchester, 2.205 Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom.
authors.forename: Andrew
authors.initials: A
authors.lastname: Hayes
authors.forename: Nianshu
authors.initials: N
authors.lastname: Zhang
authors.forename: Jian
authors.initials: J
authors.lastname: Wu
authors.forename: Philip R
authors.initials: PR
authors.lastname: Butler
authors.forename: Nicole C
authors.initials: NC
authors.lastname: Hauser
authors.forename: Joerg D
authors.initials: JD
authors.lastname: Hoheisel
authors.forename: Fei Ling
authors.initials: FL
authors.lastname: Lim
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Sharrocks
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Oliver
mesh_terms: D018929:Cell Culture Techniques / Q000379:methods*; D002455:Cell Division; D015825:Chromosomes, Fungal / Q000235:genetics; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011401:Promoter Regions, Genetic / Q000235:genetics; D012331:RNA, Fungal / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000166:cytology* / Q000235:genetics* / Q000254:growth & development
chemical_list: D012331:RNA, Fungal; D012333:RNA, Messenger