title: Promoters maintain their relative activity levels under different growth conditions.
abstract: Most genes change expression levels across conditions, but it is unclear which of these changes represents specific regulation and what determines their quantitative degree. Here, we accurately measured activities of ~900 S. cerevisiae and ~1800 E. coli promoters using fluorescent reporters. We show that in both organisms 60-90% of promoters change their expression between conditions by a constant global scaling factor that depends only on the conditions and not on the promoter's identity. Quantifying such global effects allows precise characterization of specific regulation-promoters deviating from the global scale line. These are organized into few functionally related groups that also adhere to scale lines and preserve their relative activities across conditions. Thus, only several scaling factors suffice to accurately describe genome-wide expression profiles across conditions. We present a parameter-free passive resource allocation model that quantitatively accounts for the global scaling factors. It suggests that many changes in expression across conditions result from global effects and not specific regulation, and provides means for quantitative interpretation of expression profiles.
authors.affiliation: 1] Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel [2] Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel [3] Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Leeat
authors.initials: L
authors.lastname: Keren
authors.forename: Ora
authors.initials: O
authors.lastname: Zackay
authors.forename: Maya
authors.initials: M
authors.lastname: Lotan-Pompan
authors.forename: Uri
authors.initials: U
authors.lastname: Barenholz
authors.forename: Erez
authors.initials: E
authors.lastname: Dekel
authors.forename: Vered
authors.initials: V
authors.lastname: Sasson
authors.forename: Guy
authors.initials: G
authors.lastname: Aidelberg
authors.forename: Anat
authors.initials: A
authors.lastname: Bren
authors.forename: Danny
authors.initials: D
authors.lastname: Zeevi
authors.forename: Adina
authors.initials: A
authors.lastname: Weinberger
authors.forename: Uri
authors.initials: U
authors.lastname: Alon
authors.forename: Ron
authors.initials: R
authors.lastname: Milo
authors.forename: Eran
authors.initials: E
authors.lastname: Segal
mesh_terms: D003470:Culture Media; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D015966:Gene Expression Regulation, Fungal; D017930:Genes, Reporter; D005947:Glucose / Q000378:metabolism; D008164:Luminescent Proteins / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D000097573:Red Fluorescent Protein
chemical_list: D003470:Culture Media; D029968:Escherichia coli Proteins; D005947:Glucose; D008164:Luminescent Proteins; D029701:Saccharomyces cerevisiae Proteins; D000097573:Red Fluorescent Protein